EMBO/sd-character-level-ner huggingface dataset:
WT or MARCO-/- C57BL/6 mice were inoculated s.c. in the left rear footpad with 103 PFU of ONNV (F) Tissues and serum were collected at 1 dpi and analyzed by plaque assay.
(A) Schematic representation of the annotated RefSeq gene models of LIMT (NR_002809; chromosome 12q24.31) and the neighboring protein-coding genes (RHOF and SETD1B). Arrows denote direction of transcription (note that LIMT resides on the minus strand). Also shown is the distribution of evolutionary conservation along the sequence of LIMT across 100 vertebrate species. Note that the 5' region of LIMT is highly conserved (green rectangle). Promoter-associated histone methylation (H3K4Me3) and acetylation (H3K27Ac3) were obtained in MCF7 and MCF10A cells, respectively (see Methods). Acetylation signals were obtained for MCF10A cells stimulated with EGF for 20 minutes (green), or un-stimulated (black; overlaying histogram). Note that stimulation with EGF caused a decrease in acetylation at the promoter region (red rectangle).
B: CL formation was measured in the presence of 60 nmol MLCL(18:2)3, 40 nmol PC(18:2)2, 4 µg TAZ, and 0.2 mg MBP or 0.2 mg Alb. C: CL formation was measured as in B with different amounts of MBP or Alb.
(B) Prevention of ataxia in chimeric mice. Mice were assessed for ataxia weekly during two 3-min trials on a balance beam (see Materials and Methods).
C-F Representative confocal images of ER+ (ER-0032) and triple negative tumors ( TN-0066) immunolabeled for K8/18 (yellow), CD68 (green) and Ki67 (red) (C, E) or K8/18 (yellow), CD8 (green) and Ki67 (red) (D, F). DAPI is shown in blue. Arrows depict proliferative T cells (CD8+Ki67+) or macrophages (CD68+Ki67+). Enlargements on shown in the right-hand panels. Scale bars, 200 µm for large tilescans; 50 µm for enlargements and smaller tilescans.
E. Ratios between the intensity of 47S pre-rRNA band and bands belonging to 32S or 28S rRNA species relative to panel (D) and measured at 60 minutes after the chase for both LacZ or PNRC1-expressing cells.
Confocal z-projections DIP-δ hetero- and homozygous brains in which γ-KCs were labeled by expressing membrane bound tandem tomato (mtdT-HA) driven by the γ specific QF2 driver R71G10-QF2 (γ-QF2). Larval (L3) γ-axons grow normally in DIP-δT2A-Gal4 heterozygotes (A; n=16/16) and homozygotes (E; n=24/24). In contrast, at 48hr APF and adult, γ-axons within DIP-δT2A-Gal4 homozygotes do not enter the distal part of the lobe (asterisks; F; n=8/8, G; n=20/20), while they grow normally in heterozygotes (B; n=12/12, C; n=12/12). Overexpression of a DIP-δ transgene driven by the Gal4 activity of DIP-δT2A-Gal4 (see also Figure S4) does not affect normal growth (D; n=10/10) and rescues mutant phenotypes (H; n=20/20). Note that while the R71G10 driver is consistently expressed in γ-KCs, it is also expressed in α/β-KCs in a stochastic manner. The adult γ-lobe and α/β lobes are outlined in C-D in yellow and orange, respectively, for clarity.
E, F. Spermatocytes were immunolabeled against beta-catenin (green), SYCP3 (red), PCNT (magenta), and stained with DAPI (blue). Middle columns emphasize beta-catenin signal in diplonema and diakinesis spermatocytes. Scale bars = 5 μm. G. Quantification of beta-catenin positive centrosomes per spermatocyte at diakinesis. Immunolabeling was performed on three biological replicates, with ≥20 spermatocytes quantified per replicate. The total number of cells quantified for control, Aurka cKO, Plk1 cHet, and Plk1 cKO mice were 89, 106, 122, and 93, respectively.
(A) Top panel displays structure of each CDK4/6 inhibitor tested. Bottom panel shows dose response curves with these inhibitors displaying percentage of G1-arrested RPE1-FUCCI cells. To obtain dose response curves, the number of mKO-Cdt1 positive (G1-arrested) cells were calculated following 24hr drug addition (dark blue solid lines) or 24h after subsequent drug washout (light blue dotted lines). Cmax values observed in patients (taken from (He et al., 2017; Klein et al., 2018)) are represented on each graph with red dotted lines. Graphs display mean data -/+ SEM from 3 experiments, with at least 500 cells counted per condition per experiment. (B) Percentage of G1-arrested RPE1-FUCCI cells, calculated as in panel A, but using a fixed concentration of CDK4/6 inhibitor for different durations of time, as indicated. Note, this is a fixed assay that quantifies the percentage of G1-arrested cells prior to, or 24 hrs following, CDK4/6 inhibitor washout. Each bar displays mean data + SEM from 3 experiments, with at least 500 cells counted per condition per experiment. (
ACE2-Ig potently neutralizes viruses pseudotyped with S glycoproteins from the SARS CoV and 2019 nCoV.HIVs pseudotyped with the S glycoprotein from CoVs were incubated with different fusion proteins for 1 h before infection. Luciferase activities in target cells were measured, and the percent neutralization was calculated.
(B) Mavs-/-MEFs stably expressing d2GFP were treated with recombinant IFN (200 U/ml) for 24 hrs prior to transfection or not (mock) with Cy5-labeled dsRNA, as indicated. IFN treatment was maintained for 2 days post-transfection and then GFP level monitored in Cy5+cells.
(B) Lipidomic profiling of sphingolipid metabolites in HDFs upon indicated stimulations for 2 h. Fold changes of each metabolite were calculated against corresponding controls. Heatmap shows means of 3 independent experiments. The color scale represents the relative levels of various lipids from lower (blue) to higher abundance (red).
F: Propidium iodide staining analyses revealing cell cycle distribution profiles for the samples
b, The arrow indicates a GFP-LC3+ SLAP with internal LLO expression in cells infected for 4 h. Scale bar, 5 µm.
F Western blot analysis of Viperin in the splenocytes of Usp33+/+ or Usp33-/- mice treated with mIFNβ (500 IU/ml, 12 hrs) immediately after addition of NaCl (+34 mM). Data information: Data are representative of at least two biological replicates
(A) HEK293T cells (5×105) were transfected with HA-cGAS (200 ng), Flag-STING (200 ng) and Myc-ZDHHC18 (WT or CS mutant) expression plasmids (0, 50, 100, or 200 ng) for 24 h before luciferase reporter assays were conducted. Data information: ZDHHC18(CS): a catalytic mutant with a cysteine-to-serine substitution in the DHHC motif of ZDHHC18 All data are representative of at least two independent experiments. Mean ± SEM from triplicates of technical replicates, unpaired t test; ns, not significant; **, P˂0.01; ***, P˂0.001 (A
Abundances of selected nucleotides in I91L+W133V mutant when grown for 4 hours at 40°C in M9 medium supplemented with both amino acids and 1mM dTMP. Metabolite levels were normalized to those of WT grown under similar conditions. dTDP and dTTP levels recover and are now comparable to dTMP levels. Error bars represent SEM of 3 biological replicates. The dashed line in represents value of 1 for WT.
d. Foxo1 and Foxo3 transcriptional targets expression on sorted CD4+CD25hiCD127-Tregs stimulated in the presence of vehicle or IL-12 at day 2 after stimulation (n=8). *p < 0.05, **p < 0.005, ***p < 0.0005.
Prdx4 concentration in supernatants of Prdx4 WT or KO BMDMs, primed for 6 h with LPS and pulsed for indicated time points with 5 mM ATP. Each circle represents a mean of n=3 mice, vertical lines indicate SD. **, p < 0.01; n.s. not significant (two-tailed t-test).
B During megakaryocyte terminal differentiation, AS-RBM15, activated by RUNX1 at transcriptional level, elevates RBM15protein via translation. Thus, AS-RBM15 increases the dosage range of RBM15 during MK terminal differentiation.
Distribution of BrdU track lengths in cells released for 45 or 60 minutes into S phase, respectively.
Expression of Tardbp (left), total Sort1 (center) and exon 17b Sort1 (right) mRNAs quantified by Q-PCR in micro-dissected CA1 of Tardbpfx/fx and CamKIIaCRE;Tardbpfx/fx mice after injection of EGFP-expressing lentivirus or Sortilin rescue virus. Results are presented as average ± SEM relative to levels in Tardbpfx/fx mice injected with EGFP virus, after normalization to Gapdh mRNA. (N=3 mice per condition). **, p<0.01. Data information: Results are presented as average ± standard error of the mean (SEM). All statistical tests were performed using 2-way ANOVA with Sidak post hoc analysis.
RNA sequencing analysis of the gene expression profile in IECs treated with or without LIF (50 ng/ml) for 6 hours. Statistical analysis of the average fragments per kilobase of transcript per million mapped reads (J).
d, LAMP1-YFP expressing NRK-LC3 cells as in a. Arrows show reformation tubules. e, Three-dimensional reconstruction of a cell from d.
ASK1 mRNA expression in patients with different NASH scores Data were collected in lean subjects (n=14), obese subjects (n=23) and obese subjects with type 2 diabetes (n=19). Values are expressed as mean ± SEM (D). ***
Figure 4. Sequencing analysis of the CRISPR/Cas9-induced disruption of the Tbr2 locus.(A-C) Next-generation DNA sequencing analysis of amplicons containing the Tbr2 locus and 4 off-target loci generated from PaprikaRFP-expressing cells isolated at E15.5 from neocortex of mouse embryos in utero electroporated at E13.5 with plasmids encoding Cas9_T2A_PaprikaRFP and either gTbr2 (black) or control gRNA (Con, white) as in Fig 3 A-D.(A) Quantification of the frequency of mismatches to the mouse genome sequence spanning 30 bp upstream and downstream of the Tbr2 target site and the off-target sites (OT1-4). Data are expressed as percentage of the total number of reads and are the mean of two independent experiments (8 and 5 embryos per condition, respectively).(B, C) Analysis of one of the experiments of (A) for deletions (B) and insertions (C) in the region spanning 80 bp upstream and downstream of the Tbr2 target site upon Cas9/gTbr2 plasmid electroporation.
C, D. Frequency distribution and bulk endocytic events/cell within 16 s after stimulation.
(B) Epg5 protein and the wild-type copy of Epg5 are absent in Epg5−/− mice. There is an intervening lane between Epg5+/− and Epg5−/− lanes in the Western blot.
(G) Representative survival curves of nuo-6(qm200) mutants fed with control (C RNAi) and dsRNA against cest-2.2. Data information: , the median lifespan ± SEM is reported underneath the graphs and additional information (e.g. n numbers)
A Representative images of GFP-gephyrin and GFP-G375D, expressed in hippocampal neurons at 9 + 4 days in vitro. Inset shows higher magnification. Scale bar = 20 µm.B Relative distribution of cluster density of gephyrin variants on dendrites from transfected neurons. Number of gephyrin clusters in each dendrite is normalized to 20 µm segments.
G The proportion of 41, XXY mice among the male offspring of 2-month-old Usp26+/Y, Usp26-/Y and 6-month-old Usp26+/Y, Usp26-/Y mice (n=14, 22, 10 and 8 independent experiments for the offspring of 2-month-old Usp26+/Y, Usp26-/Y mice, 6-month-old Usp26+/Y, and Usp26-/Y mice, respectively). Red dots indicate Usp26+/Y mice and green dots indicate Usp26-/Y mice.
(D) Quantification of actin intensity profile of representative siControl and siRACGAP1 treated cells shown in (A). While actin levels were uniform across the cortex at metaphase (black line), they reduced from the polar regions (Blue line - segments 2-8) in both siControl and siRACGAP1 treated cells at early anaphase.
E, F Pavement cell number and area of the third leaf at 22 DAS of GOF lines (F) that showed a significant rosette area phenotype. Data information: In A and C, data are presented as mean ± SEM, n = 3 independent experiments, *=P<0.05 (Tukey's test). In B, data are presented as mean ± SEM, n = 3 independent experiments, *=P<0.05 (mixed model, partial F-tests). In E and F, data are presented as mean ± SEM, n = 3 independent experiments, . = P<0.1, * = P<0.05, ** = P<0.01, *** = P<0.001 (Tukey's test).
(C) RT-qPCR analysis of exoc3 mRNA expression in planarians of the indicated genotypes and treatment schedule
D, Representative FA lifetime in cells treated without or with 50 μg/ml LDL (-LDL or +LDL) for 1-2 h after 24 h in 5 % LPDS. Time-lapse imaging of GFP-paxillin dynamics in cells was acquired by TIRF microscopy and maximum intensity during FA lifetime was normalized to 1. E, Analysis of FA assembly and disassembly rate of cells incubated +/-LDL as in D. Where indicated, 10 μM PF228 was added after 30 min of LDL loading. Assembly rate: n = 290 FAs (-LDL); 410 (+LDL); 192 (+LDL+PF228), disassembly rate: n = 397 (-LDL); 502 (+LDL); 214 (+LDL+PF228) pooled from 4 independent experiments. The Tukey box plots represent the median and 25th and 75th percentiles (interquartile range). The whiskers show the hightest and lowest observations. Non-parametric Kruskal-Wallis analysis of variance with Bonferroni error correction.
C Extracellular matrix quantification following trichrome staining in sg-CTRL and sg-HMGCL #2 pancreatic tumors sections (n=8 and 9 mice/group respectively, left panel). Data are expressed as mean of percentage of total tissue area ± SEM. Significance was defined by Mann-Whitney test. **: p<0.01. Representative images of trichrome staining in sg-CTRL and sg-HMGCL pancreatic tumors. Scale bar: 100 µm (right panel).
Results of coimmunoprecipitation between overexpressed LDB2 and interaction candidates LDB2 vs. RLIM (E). LDB2 (WT, T83N or P170L) and candidate interactors were tagged with Flag and HA, respectively. HEK293T cells were transfected with the Flag-construct and HA-construct indicated. After Flag-LDB2 was immunoprecipitated with a Flag antibody, the immunocomplexes were analyzed with western blotting with Flag and HA antibodies. The input samples (input) were also analyzed. Green and black arrowhead indicate positions for Flag-Ldb2 and HA-proteins, respectively.
C Kymograph of LimE (top, green) and PHcrac (bottom, red) across the dotted line in B.
Confocal micrographs of tumor EphA2-pS897 (red) and cleaved caspase-3 (H; clCasp3, green) and corresponding clCasp3 quantification (I). Scale bars: 20 μm. N = 5 mice/group.
F Volcano plot depicting the log2 of fold change versus - log10 (p-value) for Fam20C-interacting proteins in Tg-treated HepG2 cells. The red dots represent proteins showing statistically significant increase of binding with Fam20C (log2 fold change ≥ 1; - log10 (p-value) ≥ 1.3); the blue dots represent proteins showing statistically significant decrease of binding with Fam20C (log2 fold change ≤ - 1; - log10 (p-value) ≥ 1.3); the green dot is Fam20C.
b. TCR repertoire distribution assessed as clonal space homeostasis, i.e., proportion of the repertoire occupied by the clones of a given size.
Representative maximal respiration (G) of untreated- and 24 h oxaloacetate-treated adult gas-1(fc21) nematodes (Unpaired t-test, n=9-10 biological replicates from 3 independent experiments). Data information: bars represent mean ±SEM Across experiments, p value summary is ns=not statistical, *p<0.05, **p<0.01, ***p<0.001, ****p<0.0001.
Effects of CLIP170 on fusion of viral particles by endocytosis. CHME3 cells expressing Flag control or Flag-CLIP170 (D) were infected with Mock or HIV-1-VSV-BlaM-Vpr. Representative FACS analysis of cells (n = 3) showing no difference (D) from green (uncleaved CCF2) to blue (cleaved CCF2). % infected cells is indicated at the top left corner of each plot and quantification from independent repeats is presented as bar graphs at the right side of each FACS plot.
(b) Ulk1 Ser 757 is required for rapamycin to enhance the Ulk1-AMPK interaction in vitro. CBP/SBP Ulk1 proteins (wild type or S757C) were prepared from transfected HEK293 cells, which were pre-incubated with 50 nM rapamycin (Rapa, 1h) as indicated. The Ulk1 proteins were purified by streptavidin beads and the resulting Ulk1-bead was incubated with the bacterial purified AMPKα/β/γ complex. AMPKα protein levels in the in vitro pulldown assays were examined by western blot using AMPKα antibody. L.E.; long exposure.
Representative images showed SA-β-gal staining in cultured primary hOSE cells in the presence or absence of HPV E6/E7 oncoproteins. Cells were collected and stained at the 13th passage. Scale bar: 25 µm. Right graph showing the ratio of SA-β-gal positive cells in P13 hOSE cells transfected with empty vectors (CTRL-P13) or vectors expressing E6/E7 oncoproteins (E6/E7-P13).
B, C The immunoprecipitation analysis. Co-precipitation was impaired by either the WW domain deletion of ITCH or the mutation in the PPxY motifs of ENTREP. Data shown are representative of at least two independent experiments. IP, immunoprecipitation; IB, immunoblot.
B. AICD was induced in Jurkat cells as described in Materials and methods. Apoptotic cells were detected as in (A). Data represent mean ± SE of five independent experiments.
(b) Viscoelasticity of the yolk cortex. Effective complex modulus (g*) measured by indenting the surface of zebrafishembryos with AFM. Red symbols are the elastic modulus (g') and yellow symbols are the viscous modulus (g''), respectively. Standard Errors are displayed. In all the measured frequencies cortex rheology is dominated by a solid-like behavior with the viscous modulus 5 times lower that the elastic modulus. No significant frequency dependence was found in the elastic (ANOVA, p = 0.123) and viscous modulus (ANOVA, p = 0.719).
The proteasome inhibitor MG132 treatment increases LIN28A(R192G) protein level. After serum starvation for 3 hours, HEK293T cells expressing LIN28A(R912G) were treated with or without MG132 (0.1-10 uM) for 30 minutes, and then followed by WB analyses.
MEF cells were fixed before (control) and following S-HAD treatment (10 µM, 4 h) then nuclei (DAPI), cyclin C (indirect immunofluorescence) and mitochondria (MitoTracker Red) were visualized by fluorescence microscopy. Merge panels present DAPI staining (blue) only. S-HAD peptide activity requires cyclin C. The experiment described in A was repeated with Ccnc-/- MEF cultures.
(A) Volcano plot analysis of transcriptomic changes where statistically significant genese are delimited by a horizontal line. Decreased genes are represented in red while the up-regulated ones are in green, while genes that were not statistically significant are represented in black.
C. The effect of carbon source depletion on COPI•Dsl BiFC signal polarization. Cells carrying Dsl1pVN•ε-COPVC were starved in glucose-free PM+ura medium for 90 min. Then the medium was replaced by PM Glc+ura with 2 % glucose, while imaging the cells continuously at 1 min intervals. Two exemplary cells are shown (upper and lower panel). Starvation-induced dispersed BiFC signals reversibly returned to polarized distribution within minutes after addition of glucose-containing medium. Arrowheads mark the point of signal repolarization, arrows indicate resumed bud outgrowth. Scale bar 5 µm.
(B,C) A scenario simulating the presence of four SNARE complexes near the fusion site. The modeled indentation corresponds to a relative indentation of -1.6 nm (see Fig. 2B). This corresponds to an exaggerated indentation force of about 80 pN which we exploit to demonstrate the clustering between "indentations" within our limited simulation time. The C-terminal amino acid of each Vam3 and Nyv1 is represented by a red or blue bead, respectively. (B) Isolated SNARE C-termini with short peptide tag. The C-termini concentrate in a small zone (similar membrane perturbations attract each other). (C) Steric hindrance by the addition of bulky proteins prevents collective, localized force transduction by multiple SNARE complexes.
Human first-trimester trophoblast cell line Sw.71 (left panel) and human primary culture (right panel) trophoblast cells were infected with ZIKV (MOI=2) for 1 h and refreshed with regular media over time. RNA was collected for measuring gene expression by qRT-PCR. Data represent as mean ± SEM; n=4 biological replicates. NT, no treatment group; HPC, human primary culture. (B) IFNα is not highly induced in response to ZIKV infection in trophoblast cells. IFNα mRNA expression was inhibited in the first 24 h.p.i. and maintained at low level during ZIKV infection. Difference not significant (n.s.) by One-way ANOVA.
(B and C) H1299 (C) lung cancer cell lines stably expressing the indicated constructs were counted with Trypan blue for several days following stress stimuli (thapsigargin (Th) for H1299). Data was normalized against 1st day values. Δ160p53 shows similar pro-proliferative capacities as mutant R273Hp53. On the other hand R273Hp53 lost pro-proliferative functions when deficient for Δ160p53 expression (M160AR273Hp53).
(D) Schematic of immunoprecipitation and mass spectrometry experiments aimed at identifying CGG repeat RNA interacting proteins Growth media, containing different isotopes of lysine and arginine for SILAC labeling, are indicated as light (Lys-0 and Arg-0) and medium (Lys-4 and Arg-6).
C In vitro acetylation assay was performed as described in A. The reaction products were resolved by SDS-PAGE and acetylated p53 was purified from the SDS-PAGE and subjected to mass spectrometry analysis.
E: KI cells synchronised in mitosis with either nocodazole (M Noc.) or STLC (M STLC) were collected by shake-off, and drug-treated cells that remained adherent after shake-off (AS Noc.; AS STLC) were lysed and subjected to GFP TRAP IP. AS cells and free-GFP-expressing 2G-PAI1 U2OS cells were included as controls. Input and IP samples were analysed by IB with the indicated antibodies. Data information: All blots are representative of at least 3 independent experiments.
(B) Time course changes of Fstl1 protein expression in NRCFbs after stimulation of recombinant TGF-β1 (10ng/ml). Protein expression of Fstl1 was detected by immunoblotting. Tubulin was used as a loading control (n=3 for each time point). Two independent experiments were performed.
H Quantification of cleaved caspase 3 positive hepatocytes treated with or without rapamycin. More than 100 cells per replicate were analyzed in a blind fashion (n=3 independent experiments). Data information: data are presented as histograms showing the mean ± SEM. Error bars show minimum and maximum values.
Body weights of mice fed the HFD for the indicated interval. Two cohorts were utilized, one measured at 4 and 8 wk and the other at 10 and 16 wk; n=16-20.
I. A model summarizing the results in Fig 3 (left half) and speculating a switch role of endogenous Rabl2 for ciliary GPCR export and signaling, taking the Hh signaling as an example (right half). The GTP-locked Q80L mutant represses the export of ciliary Gpr161 and Smo, leading to reduced Gli-A and possibly increased Gli-R formations and accordingly attenuated Gli1 expression. Endogenous ciliary Rabl2-GTP would similarly repress the export of Gpr161 and Smo until it was converted to GDP-binding form through GTP hydrolysis. Proper regulation of the GTP hydrolysis would therefore facilitate proper Hh signaling.
(F) qRT-PCR analysis of the mRNA levels of the indicated genes in cells with different types of ESM1 overexpression. Differences in mRNA levels compared with vector cells are shown as fold changes presented as the mean ± SD of three independent experiments. *
Composite profile of Rrm3 occupancy across the average ARS plotted as Rrm3 percentage of significant ChIP hits per segment. Each ARS was divided into 11 equivalent segments from the start and end coordinates. The average signal log2 ratio for Rrm3 significant hits that map on each segment was plotted.
(B) MG132 and SUMO-2 cause mutant HTT to accumulate as HMW species (bracke and asterisk). Western blot showing IP with HTT antibody crosslinked beads from the detergent-insoluble fraction probed with the anti-HTT antibody.
(c) Lysozyme IHC demonstrating increased lysozyme positive cell numbers in tumours from Lgr5 Apc Huwe1 mice. Scale bars = 200 µm (low magnification), 100 µm (high magnification inset). (d) OLFM4 IHC demonstrating expanded stem cell population in Lgr5 Apc Huwe1 tumours. Scale bars = 200 µm (low magnification), 100 µm (high magnification inset).
Reducing SDS-PAGE of SEC purified UFE digests with indicated molecular weight markers. The different SEC elution volumes of F1 and F2 (A) reflect different levels of egg coat filament digestion by HCE/LCE.
Volumes of the binding pockets visualised by the van der Waals spheres of the ligand and coordinating residues of MhsT in complex with L-Phe, L-4-F-Phe, L-Tyr, L-Val, L-Leu and L-Ile.