EMBO/sd-character-level-ner huggingface dataset:
E. Average velocity of MB (endo) and cy3-pre-miR-181a-1 (exo) puncta. Each data point corresponds to one punctum. Total number of puncta and axons analyzed: 353 puncta, 20 axons (endo), 484 puncta, 29 axons (exo). n=3 (endo), n=4 (exo) independent experiments. Values are median with interquartile range. Abbreviations: MB, molecular beacon; ns, not significant; antero, anterograde movement; retro, retrograde movement.
(D) Immunoblot analysis of TLR2 and pS6 in cell lysates from HaCaT keratinocytes carrying either a vector expressing TLR2 or an empty vector were exposed to LL37 (4 μM) for 2 h. pS6 protein levels were analyzed relative to total S6. Tubulin or Actin was used as the loading control.
(D) α-KG restores Rad53 phosphorylation in snf1Δ. CBB indicates coomassie bright blue (CBB) staining of the membrane as the loading control.
(A) 293T cells were transfected S proteins with each variant-associated mutation for 24h and stained with biotinylated ACE2 and fluorescent streptavidin before analysis by flow cytometry.
(E) Plasma concentrations of MK-2206 and 14h were analysed in samples obtained 2-3 hours after the administration of the last dose on the 24th day of treatment. Results are presented as a mean ± SD from three different samples.
(E) RNA-binding activity of DDX43 variants as analyzed by EMSA. Upper: The GIDN mutant was substituted G90 and I96 conserved within the KH domain to Asp and Asn, respectively. Lower: A 40-nt single-stranded RNA was 5′ end-labeled with 32P and incubated with DDX43 variants in the presence or absence of 0.1 mM ATP. Supershift means non-canonical complex.
Hypotonicity‐stimulated cisplatin uptake in HEK WT cells was selectively blocked by 100 μM carbenoxolone (CBX), a non‐specific blocker of VRAC (n = 3).
A-B Seqminer heatmaps of MYC and Omomyc levels around TSSs of all MYC promoter-target genes in BT168FO (A) cells, treated or not with Dox for 24 h. TSS regions are ranked by decreasing MYC occupancy in untreated cells. Each row shows the ± 5 kb region centred on TSSs. Colour scaled intensities are in units of tags per 50bp. The plots adjacent to each heatmap depict MYC and Omomyc binding patterns at genes in the two gene clusters denoted by arrows, in cells treated or not with Dox.
C. Average percentages of cells in each phase of the cell cycle phases for each of the indicated HSPC subsets from WT and PKCδ KO mice. Data are pooled from two independent experiments (totaling n=6-7 mice per genotype). Data information: All data are presented as mean±SEM, *p<0.05 and **p<0.001, with significance determined by two-tailed Student's unpaired t-test analysis.
(A) Time-lapse microscopy was used to measure cyclin-Citrine levels during mitotic exit in unperturbed cell cycles. The cells were synchronized by the nuclear import of 50% of Whi5-mCherry at mitotic exit. The plot shows mean ±SEM fluorescence intensities averaged over a population of cells. The vertical line at -14 minutes marks the estimated time of anaphase entry.
F Total cellular protein levels of PD-L1 (top) and GAPDH (bottom) in U2OS polyclonal MLLT6 knockout or mock control cells with and without IFN-γ stimulation. Numbers indicate relative band intensities of PD-L1 protein normalized to GAPDH.
In TMXHIGH cells, the undisturbed ER-mitochondria contacts allow Ca2+ and lipid transfer and thus optimal mitochondrial function. Here, mitochondria and NOX4 generate no or low levels of ROS which can be eliminated by mitochondrial/cellular antioxidants. ORAI channel-governed SOCE activates NFAT1 translocation by its dephosphorylation through calcineurin and initiates the expression of target genes promoting melanoma proliferation and migration. NFAT1 controls the gene expression of mitochondrial proteins, thus suggesting a regulatory mitochondria-NFAT1 feedback loop.
(L) Flow cytometric analysis of CD22 surface expression in resting or stimulated B cells with 10µg/ml anti-µ chain (Jackson ImmunoResearch), 1µM or 10µM LatA for 5 and 15 minutes. Error bars denote mean ± SD.
D) Larval brains at 24 h ALH from control (grh-Gal4 UAS-CD8-GFP + UAS-nod-lacZ) and msps810,UAS-nod-lacZ under the control of grh-Gal4 UAS-CD8-GFP were labeled with β-Gal, Dpn, and GFP. Quiescent NSCs in the central brain were shown. Arrows point at the localization of Nod-lacZ in qNSCs. E) Quantification graph of Nod-β-Gal localization in qNSCs from genotypes in (D). n=55 NSCs for control; n=45 NSCs for msps810. ****p<0.0001
H Nuclear/Cytoplasmic fractionation and western blot analysis in mouse prostate organoids for selected signalling mediators in the presence or absence of SB203580 (p38α/β inhibitor; 10 μM, 24 hours).
Western blot for p53 pS15, p53, and vinculin in PHD1-silenced p53R248/− HCT116 upon 8-h treatment with 300 μM 5-FU.
A. Time-lapse analysis depicting invading RH adfcKD parasites expressing Cb-EmeraldFP. A F-actin ring can be observed at the TJ in the majority of cases (red arrowheads, first panel). Invasion can also occur without formation of an F-actin ring (second panel). During capped invasion, an F-actin ring is formed (third panel). Invasion of adf cKD parasites occurs without formation of an F-actin ring (fourth panel). F-actin accumulation is observed at the posterior pole of the parasite in all cases (orange arrows). Green segmented lines depict the area that was measured for generation of intensity plot profiles shown in (B). Yellow and purple dotted lines indicate the extra- and intracellular part of the parasite respectively. B. Intensity plot profiles of the movies shown in (A). Depicted plots correlate to half-invaded parasites. In the case of F-actin ring formation, two distinct peaks are detected, correlating to the F-actin ring at the TJ (red arrowhead) and the posterior pole of the parasite (orange arrow). In the case of no F-actin ring, no accumulation at the TJ can be observed; only the peak correlating to posterior F-actin can be detected. For adf cKD, only one peak can be seen corresponding to the posterior pole of the parasite. C. Quantification of F-actin accumulation at the TJ for RH Cb-EmeraldFP parasites as detected in time lapse analysis. The values are expressed as percentage. 28 total parasite invasion events were captured across three different biological replicates. Two-tailed unpaired t-test analysis was performed. **** p value <0.0001. Data information: Error bars represent standard deviation. White arrows point to direction of invasion. Scale bars represent 5 µm. ****p value <0.0001.
(i) Representative plates from Alu-retrotransposition assay transfected with control siRNA or siRNA-targeting ATG5.
(g) Midguts dissected from animals expressing Atg4DN specifically in DsRed-marked clones of cells at puparium formation and analysed by fluorescence and differential interference contrast microscopy. Representative images are shown. (h) Cell size quantification (μm2) from g, n = 10 animal intestines per genotype with 1-5 cells measured per intestine.
Scatter plot and correlation coefficient (r) of ASK1 mRNA expression and ATG12 mRNA expression. 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). ***
B, C Immunofluorescence images of sarcomeric α-actinin and myosin (B) and assessment of cardiac function (C) in homozygous Ttn knock-in embryos cultured for 24 h after mScrAON and mTtnAON transient transfection (n = 3 per group) or lentivirus delivery (n = 7 per group). Scale bars, 10 μm.
Confirmation of RNA-seq data via qPCR on pure hepatocytes isolated via flow cytometry-based sorting (n = 3/group). (E) Ppara and (F) Hmgcs2 mRNA expression is shown as relative expression, normalized to housekeeping genes Hprt and Rpl. P-values were calculated using 2-way ANOVA analysis.
E) Tlk2Δ cells were generated using CRISPR/Cas9 genome editing. Cells were synchronized in G2 by thymidine release, damaged with 0.5 μM Adriamycin for one hour. After a 16-hour G2 arrest cells were induced to recover by addition of caffeine for 8 hours and analyzed by FACS. Error bars represent SD, n=4. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, * for P≤0.05, *** for P≤0.001).
c. Feature plot of UMAP of single cells from pseudotumor CSF shown in Figure 1a, depicting cell-wise representations of indicated transcripts. Relative expression shown.
(B) Akt was immunoprecipitated from the soluble fraction of muscles from fed or fasted (2d) mice. Percipitated were analyzed by immunoblotting using an anti-ubiquitin conjugates. Mouse IgG was used as a control for non-specific binding.
(F) Significant methylation changes of specific TEs subdivided in different classes of TEs (calculated using logistic regression function of Seqmonk, padj < 0.05; data are represented as medium smoothed violin plot with indicated median and quartiles as dotted line).
Whole-plant recordings of changes in stomatal conductance (gs) from self-grafted donor lines (WT/WT, stp1stp4/stp1stp4) and reciprocal grafting of shoot/root (WT/stp1stp4, stp1stp4/WT) plants. Data shown are means ± SEM; n = 3 per genotype.
D. Schematic of the experiment shown in (E-G). ΔN-CENP-B protein was fused to dCas9-doxycycline (Dox) inducible protein and was inserted at a single genomic locus in DLD-1 CENP-A-/EA male cell line expressing a gRNA targeting centromere Y.
Analyzing single cell transcriptomic database of the E14.5 mouse cortex, showed the specific expression of Rgcc in NSCs. Data were downloaded form http://zylkalab.org/datamousecortex.
(b) Size-exclusion chromatography data of NDP52-GAL8-LC3C complex. The first peak (marked by an orange bar) represents the ternary complex, as shown by the SDS-polyacrylamide gel electrophoresis (SDS-PAGE) results marked by an orange bar (lane 1, 2 and 3). The second merged peak (marked by green and yellow bar) and corresponding SDS-PAGE results show the remaining free GAL8 (lane 4, 5, 6 and 7) and LC3C (lane 5, 6, 7 and 8).
C sgRNA frequencies (log2 of fold change) in viability screen. sgRNAs targeting controls are highlighted; essential (orange), non-essential (blue). Genes attributed to PD-L1 modulation are shown in different colors (red, yellow and purple).
(D) Ribbon diagram illustrating structural model of an octamer SPOP assembly. In a 27 µM SPOP solution three percent of the oligomeric assemblies would be equal in size or larger. The domains are colored as in Figures 1 and 7A (MATH, green; BTB, red; BACK, blue), with alternating monomers shown in gray for clarity. The model was built using two available crystal structures (PDB ID 3HQI (Zhuang et al, 2009) and 4HS2 (van Geersdaele et al, 2013)), and no further assumptions.
Ndrg4+/+ and Ndrg4-/- mice have a similar bodyweight (n=17 vs. 14 in A and n=25 vs. 19 in B).
A, B Western blot analysis of heart and quadriceps lysates using anti-GAA detects both the precursor GAA (110 kDa) and the mature lysosomal GAA (70 to 76 kDa) forms in muscle of NHPs treated with (A) AT845 (n=3) or (B) Cyno-AT845 (n=3) at 2×1014 vg/kg. Each tissue was analyzed in triplicate, and each respective symbol indicates use of a vehicle control heart tissue (^) or a vehicle control quadriceps tissue (*). (See also Appendix Table S3)
Mice were injected with control (Ctrl) or STING-KO MC38 cells, and subjected to treatments, with each dose consisting of 25 mg/kg, 50 mg/kg or 75 mg/kg 5-FU, or PBS. C. Tumor and spleen weights at the endpoint for (B), with each dot representing a mouse.
(H) Representative confocal microscopy images of untreated and amino acid-starved (4 h) MCF7 cells stained for endogenous CIP2A and raptor. Black lines indicate that intervening lanes have been spliced out. −AA, amino acid starvation; IP, immunoprecipitation; a.u., arbitrary unit. Bar, 10 µm.
(A) MSD, MPS‐IIIA and WT MEFs were subjected to a triple labelling with anti‐VAMP7, anti‐Vti1b and anti‐LAMP1 antibodies. The merges between VAMP7 and Vti1b (double merges in yellow) and between VAMP7, Vti1b and LAMP1 (triple merges in white) are shown (see also enlarged images showing the extent of co‐localization in different regions of the cells). The VAMP7-Vti1b co‐localization was quantified in 15 different cells and displayed as % of Vti1b co‐localizing with VAMP7 (means±s.e.m.).
(D) WT (SCY62) and tag∆ste∆ (H1246) cells expressing GFP−Atg8 were grown to mid-log phase in YPD and shifted to SD-N for the indicated time periods. Cell lysates were subjected to SDS−PAGE, followed by western blot analysis using anti-GFP, anti-Ape1 (prApe1, premature Ape1; mApe1, mature Ape1), and anti-Fas1 and anti-Pgk1 antibodies.
Scheme of the experiment assessing short-term homing of HSPC to HO-1 deficient niche.
(D) Representative images of tyrosine hydroxylase (TH)- positive neurons (scale bar = 1 mm). The areas delineated by the white boxes are magnified in the insets. The yellow arrow indicated misoriented TH-positive axons (magenta: TH).
(D) The effect of PIK-III + Dynasore or DMSO on the growth of S. aureus USA300 in RPMI with 5% (v/v) FBS is shown. The data are the mean OD600nm +/- standard deviation of four biological replicates of S. aureus for each condition and are representative of three independent experiments.
(B) Rad53 hyperphosphorylation of WT and snf1Δ in response to HU. Cells were synchronized in G1 and released into the fresh medium containing 200 mM HU for the indicated time. Cell extracts were prepared for immunoblotting against anti-Rad53 antibodies. Tubulin was probed as a loading control.
MA plot of log2[glucosamine-treated/untreated, M] plotted over the mean abundance of each gene (A) at 12 hpi. Transcripts with a significantly higher (above x-axis) or lower (below x-axis) abundance in the presence of glucosamine are highlighted in red (q ≤ 0.05). iswi is highlighted in blue (q = 6.71x10-10) and the active var gene is highlighted in green (q = 2.53x10-5). Two and three replicates were used for untreated and glucosamine-treated parasites, respectively. p-values were calculated with a Wald test for significance of coefficients in a negative binomial generalized linear model as implemented in DESeq2 (Love et al, 2014). q = Bonferroni corrected p-value.
A) Pictures of YES plates with G418 showing growth of G418 resistant subclones in fft3D (PP3) and fft2Dfft3D (PP4) mutant strains with new integrations of Tf2-12-neoAI. After 3 days at 32o C.
D: We hypothesize that remodeled CL stabilizes the deformation of the bilayer because it has both intrinsic negative curvature (wedge-shaped molecule) and high protein affinity. By stabilizing bilayer deformations, remodeled CL increases the cohesion of protein-crowded membranes.
E Higher hydroxide peroxide levels in Tsc2-deficient MEFs across different numbers of seeded cells (X-axis). Significance corresponds to two-way ANOVA test (P = 1x10-4; replicates/condition n = 2, independent experiments n = 2). The bars indicate mean ± SD.
(I) High magnification of representative HCs from P1 WT and Elp3cKO cochlea stained for F-actin and gamma-tubulin (white). The basal body of kinocilia is shifted centrally at the apical surface of Elp3cKO HCs. Scale bars=2µm. Polar plotting of kinocilium basal body position for each row of HCs of WT and Elp3cKO (WT/KO IHC: n= 42/32; OHC1: n= 47/48; OHC2: n= 47/45; OHC3: n= 44/44; cumulative data collected from 3 animals per genotype). Cellular orientations were tested using Watson U2 test (p<0.001 between WT/Elp3cKO, for all HC rows) and the mean vector lengths, determined from the cell centre to the basal body, were compared using t-tests (p<0.001 between WT/Elp3cKO, for all HC rows).
Left: Representative live-cell fluorescence imaging of EGFP-EB1 in control, CAMSAP2 siRNA transfected and centrinone-B (500 nM, 7 days) treated hRPEs. Scale bar: 20 μm. Right: Quantification of EB1 growth speed obtained by plusTipTracker. Vinlin plot center lines denote the median, and dashed lines represent the 25th and 75th percentiles.
(c) RT-qPCR analysis of AluYa5 and AluYb8 in 250-350 nt RNA isolated from cells treated with siRNA-targeting ATG5 or control (10 nM, 48 h, n=3, *P=0.046 AluYa5, P=0.043 AluYb8, ANOVA).
B) Volcano plot representing the statistical analysis of the data from the screen, where the y axis represents statistical criteria and the x axis the fold change in luminescence units.
(F) HeLa-GFP-Parkin cells expressing mCherry-NDP52 mutants were incubated with 1 µM valinomycin and 100 nM bafilomycin A1 for 3 h. Cell lysates were subjected to immunoprecipitation using anti-RFP magnetic beads. Immunoprecipitates were analyzed by western blotting. Data are representative of three independent experiments
(c) Comparison of the GuHCl-induced chemical unfolding of the secondary structure (black), monitored by far-UV-CD at 222 nm, and tertiary structure (green), monitored by Trp-fluorescence, of BclxLΔTM (left) and BakΔTM (right). The native (N), intermediate (I) and unfolded (U) states are indicated at the top.
(D) Representative immunoblots for pPERK, cleaved-ATF6, and GAPDH, and relative protein levels of pPERK and cleaved-ATF6 in control (open bars) and Brucella-infected (solid bars) cells. GAPDH was used for normalization. The intensity of the bands was quantified using the MultiGauge software, and the results are shown in the bar graphs. As a positive control for activation of PERK or ATF6, HeLa cells were treated with 5 μg/ml of tunicamycin for 8hr ('Tm'). The protein levels at time 0 hr were assigned the value 1. Data are means ± SD from three independent experiments.
A, B Regression plot showing the association between baseline AV45 PET (x-axis) and annual AV45 PET change (y-axis) across the entire sample (N=300). The vertical dashed line represents the Aβ-positivity threshold of AV45 PET SUVR > 0.079 (A). Regression plot for the association between baseline AV45 PET and annual AV45 PET change stratified by baseline CSF sTREM2 levels (B).
(e) Immunoblots of Triton X-100 soluble ('TX100') and insoluble ('1% SDS') fractions of cerebella obtained from control and Miz1ΔPOZNes mice of the indicated ages. Blots were probed with antibodies recognizing either mono- or polyubiquitinated proteins. Staining of the membrane with amido black was used as loading control.
The Venn diagram showing genes with significantly isoform changes. Pink circle represents genes with highly expressed isoform (FPKM > 5) that emerged during EPC generation. Blue circle represents genes exhibiting isoform proportion changes (delta iso > 0.15) after PLB treatment (PLB vs DMSO). Green circle represents genes with differentially expressed isoforms (FC > 10 & FDR < 0.05) after PLB treatment (PLB vs DMSO). The heatmap shows the expression of the overlapped genes ranked by FC when compared between DMSO vs PLB treated cells. The heatmap was scaled with Z-Score using the log2(FPKM) expression of isoforms of indicated genes. n=2 technical replicates
(D) Quantification of pERM intensity across the perimeter of the cells as shown in (B) where 5 and 6 represent regions closest to DNA, and 1 and 10 furthest. DMSO (n=28 cells) show increase in pERM levels away from the DNA, cells treated with ZM447439 (n=26 cells) during exit, fail to polarize the pERM proteins. Data presented as mean ± SD.
(C) Treatment with 1,25D3 or RA transiently enhances co‐immunoprecipitation (IP) of p19INK4D with cyclin‐dependent kinase CDK4 in U937 cells. Similar results were obtained in SCC25 cells (not shown). A control western blot (W) of CDK4 levels in ligand‐treated cells is shown below.
, B. survival of Ssrp1fl/fl; CreERT2+/+ mice of different ages (weeks) after the start of tamoxifen (TMX) treatment. B. Kaplan-Meier survival curves. Log-rank test p = 0.032 for the oldest male age group versus all other male groups; p = 0.013 for all females versus all males; for all other comparisons p > 0.05. n = 6-10 mice.
B) Left panel: Schematic representation depicting the genomic structure of the strains used to evaluate repair pathway choice. The location of a MAT specific probe and the restriction endonuclease cleavage sites used for Southern blot analysis to detect repair product formation are indicated. Note that the use of NHEJ or HR generates different product that can be recognized in Southern blots by the different disposition of the restriction sites for the endonucleases used. Arrow depicts the localization of the double-strand break. Right panel: Physical analysis of wild-type and cdc14-1 cells harbouring the repair pathway choice assay. Cells were grown overnight and HO induction was attained through addition of galactose for 1.5 hour at semipermisive temperature. After induction of the HO, glucose was added to repress the HO expression and samples were taken to analyse repair efficiency. DNA was extracted, digested with EcoRV, separated on agarose gels and blotted. Blots were hybridized with a probe corresponding to the MATa-only DNA sequence. A second probe to the HIS3gene was used to control the amount of genomic DNA loaded at each time-point. Graphs show quantification of mating type switching by gene conversion (HR), restoration of MATa (NHEJ) and the kinetics of the DSB induction. All data was normalized with the HIS3 gene. Graphs show the mean ± S.D. from three independent experiments. Replicates were averaged and statistical significance of differences assessed by a 2-tailed unpaired Student t test.
(E) uORF translation is correlated with CDS repression. Scatterplot displays the per-sample mean repression of uORF-containing transcripts versus the mean translation efficiency of uORFs in single-uORF transcripts. Repression is determined by calculating the difference between the mean TE of CDSs in uORF-containing transcripts versus the mean TE of CDSs in transcripts lacking uORFs/oORFs in their TLS. Only expressed transcripts (>0.5 RNA RPKM across samples per organism) were counted. Labels indicate the sample name. For more information on individual samples, see Expanded View Table EV3.
E. The cell plasma membrane localization of PTENε is required for its interaction with downstream targets. FLAG-tagged CDC42, VASP, ACTR2, or FSCN1 plasmid was co-transfected with a plasmid expressing PTENε with or without 69-81aa deletion carrying C-terminal S-tag and HA tag in HEK293 cells. Cell lysates were incubated with S protein agarose before western blotting with antibodies against the FLAG tag and HA tag.
Western Blot of Chk1 in U2OS cells, 48 h after transfection with siRNA. Actin was used as loading control.
(A) Endogenous FAM134B forms oligomers. FAM134B knockout (KO) or wild type (WT) 293T cells were treated with 1μM of Thapsigargin (Tg) for different time and the cell lysates were prepared and analyzed by Western-blot.
L-N, Effect of Scaf1 loss of function on female fertility. (L) Number of eggs per clutch (Δ1 +/+ n=12, Δ1 -/- n=13, Δ2 +/+ n=13, Δ2 -/- n=10). (M) Quantification of mature ovary follicles per ovary section (average of three sections/biological replicate) (Δ1 n=5, Δ2 n=8; same number of animals for homozygous scaf1+/+ and scaf1-/-). (N) Representative images of H&E-stained ovaries. Dotted lines delineate adipose tissue.
Protocols of HDAC1 activator treatment and behavioral tests. WT or FTLD-TDP Tg mice (6-mon-old) were i.p. injected with HDAC1 activator 5104434 for 2 months (6 mg/kg/day), following which they were subjected to a series of behavioral tests and then sacrificed for further examination.
A, B. Representative images and analysis of AIF accumulation in the nuclei of HME control (vec) and OAS single-knockout cells (KO), and HME control (vec) and OAS double- and triple-knockout cells (DKOs and TKO), 24 h after treatment with 1000 μM H2O2. Data information: Nuclei were visualized by DAPI staining. Arrowheads: AIF translocated to nuclei. Untreated control cells are shown on the left. Right panels, AIF-positive nuclei were counted from pictures taken from three independent fields in two independent experiments. Means ±SD are plotted. HME: * p<0.005; ** p<0.001 compared to H2O2-treated control (vec) cells;