EMBO/sd-character-level-ner huggingface dataset:
(a) The proportions of EGFP-positive MEFs with aggregates, transfected with EGFP-HDQ74 and pcDNA3.1 (empty vector) in Atg5+/+ cells, or transfected with EGFP-HDQ74 and pcDNA3.1, WT Atg5 or K130R Atg5 constructs in Atg5-/- cells for 4 h (1:3 ratios), were treated for next 48 h with or without 10 μM calpastatin. All data are from the same experiment, but odds ratios for reference conditions in specific experiments have been set to 1, to facilitate comparisons. Atg5-/- cells had increased EGFP-HDQ74 aggregates compared to Atg5+/+ cells. Error bars show 95% confidence interval.
D. Confluence over time of BT20, T47D, and BT549 transfected with HA-FGFR2b stimulated with FGF7 (dark green) or FGF10 (burgundy). Data represent the mean ± SD of N=3 compared to FGF10. P value = <0.05 *, <0.01 **, <0.001*** (Student's t-test).
(B) The degradation of Far1(1-150)-GFP with either wild-type or all serine-based phosphorylation sites and the indicated docking motifs was measured in time-lapse microscopy. Plot shows mean±SEM of GFP fluorescence intensities from Start.
(H) Epistatic relationship between ZBTB7B and RSK3 in terms of ATXN1 regulation. ATXN1 levels were measured after overexpression of ZBTB7B in the RSK3 knockout cell line (sgRSK3) and control cell lines (WT and sgControl) (n = 3). ZBTB7B+RSK3: co-overexpression of both ZBTB7B and RSK3. Data information: Mean ± SD, *P<0.05, **P<0.01, ***P<0.001 ****P<0.0001, one-way ANOVA.
E: Cells were treated as in (D) and collected at the indicated time points for western blot analysis of Mad1-3HA. Cyc: cycling cells.
(a) Diagram of AR truncation constructs. N-term, N-terminal; C-term, C-terminal; m1-m4, mutants 1-4; NTD, N-terminal domain; DBD, DNA binding domain; Hinge, hinge domain; LBD, ligand binding domain.
(G) Representative immunohistochemistry staining pictures of CD3+ T cells in colon tumors (The scale bars represent 400 μm ).
Groups of BALB/c mice (n = 5) were inoculated three times, four weeks apart, with 20 µg of the postfusion F proteins indicated above each panel. One group (n = 5) was inoculated only with the CpG adjuvant, as indicated. Two other groups of mice (n = 8) were similarly inoculated with either F-415 or F-416, as indicated at top of the panels. B) Five days after virus inoculation, mice were sacrificed and the amount of virus in lung extracts was measured in a plaque assay. Mean virus titer for each group is indicated by short horizontal bar.
B. Representative images of syncytia formation assay. Large syncytia were observed for NTC and ADAM17 KO cells, but were strongly reduced when ADAM10 was knocked-out, either alone or together with ADAM17 or upon inhibition with BB94 (10 µM). For both ADAMs, the cell lines obtained with gRNA sequence 1 were used. Images show GFP fluorescence and Hoechst staining. Scale bars, 50 µm. C. Quantification of images from fluorescence microscopy (B). Left plot: the area of the fused cells in green (GFP) was quantified and normalized to the Hoechst signal (blue) of the entire image to account for differences in cell density. Right plot: The nuclei within syncytia were determined by calculating the ratio between the Hoechst signal within syncytia and the total Hoechst signal in the entire image. The data are normalized to NTC DMSO (N >= 8). Two-way ANOVA with Tukey's correction for multiple comparisons. All data are represented as means ± 95% CI of at least 3 independent experiments. **p < 0.01, ***p < 0.001.
F. GSEA plots of DEGs for early-fetal gene sets. G. GSEA plots of DEGs for late-fetal gene sets.
D Primary rat ventral spinal cordneurons were prepared and after 4 daysin vitro (DIV) transfected with GFP alone or together with the indicated PDIs constructs. Cells were fixed at 10 DIV and SMI32 staining was performed to identify motoneurons. Images were taken and the total outgrowth of GFP and SMI32 positive cells was quantified. Results are compiled from 3 independent experiments.
d, MIP image of wt retina transplanted with P8 Nrl.Gfp+/+ x myrRFP/+ photoreceptors; showing wt host ONL photoreceptor labeled with cGFP (green) but not with myrRFP (red); Scale bar = 50µm; e, quantification and statistical analysis of material transfer events following subretinal transplantation of live (cGFP = 3775 ± 804, myrRFP = 436 ± 145) or UV-treated (cGFP = 1.3 ± 2.5, myrRFP = 4.3 ± 5.7) Nrl.Gfp+/+x myr-Rfp+/+ photoreceptors into wt hosts (N = 8 and N = 4 retinae, respectively); One-way ANOVA, parametric, two tail, Tukey's multiple comparisons; Graph shows mean ± S.D.
(C) Effects of HDAC6 overexpression or CAMDI co-expression on the centrosomal localization of γ-tubulin. HeLa cells co-transfected with Centrin2-EGFP with/without HDAC6-HA and FLAG-CAMDI were immunostained with anti-EGFP (green) and anti-γ-tubulin antibodies (red). DNA was stained with Hoechst 33258. Scale bar, 1 μm.(D) Quantification of intensity of γ-tubulin at centrosome. n = 39, 16, 17 cells. *, p<0.05, **, p<0.01, One-way ANOVA with Bonferroni's post hoc test. Data are presented as mean ± SEM.
(B) Sociability and social recognition memory in AppNL-G-F (KI) mice and C57Bl/6J wild type (WT) controls were tested using a standard protocol (top). During sociability, control (grey plots) and AppNL-G-F (colored plots) mice showed more interest in a strange mouse in an adjacent testing chamber [S1] than in an empty chamber [E]. This behavior was similar irrespective of VHH-B9 or GFP treatment. Social recognition memory (preference for a novel mouse in S2 over S1) was observed in controls (grey plots) expressing VHH-B9 or GFP. In AppNL-G-F mice (magenta plots), VHH-B9 prevented deficits in social recognition memory. Data are presented as violin plots. Median and quartiles (thick and thin white lines respectively) indicate spread of data. Sociability *p=0.01, ***p=0.0005, ****p=0.0001; Preference for social novelty *p=0.04, **p=0.006, (2-way ANOVA with post-hoc multiple comparisons using Šídák correction). Behavioral experiments with AppNL-G-F: AAV-VHH-B9, n=17; AAV-GFP, n=16. Experiments with C57Bl/6J mice: AAV-VHH-B9, n=18; AAV-GFP, n=18, non-injected, n=18.
(B) Merlin-depleted LN229 cells were reconstituted with wild type (WT) Merlin or its mutants, treated with DMSO or thapsigargin (TG), and subjected to western blotting. The ratio of mono-ubiquitinated to native Merlin in each lane was quantified by Image J and is shown under the blot.
(E) Hematoxylin and eosin (H&amp;amp;E) staining of spleen isolated from WT and FAKΔmyeloid mice 5 days post-infection with S. typhimurium strain SL1344. Arrows indicate areas of leukocyte infiltration. Lesion indicated by yellow arrow is outlined in the higher magnification panel to the right. Bars represent 200 µm and 50 µm.
(a-c) In situ structures of the 96-nm repeat from pig (a), horse (b), and mouse (c) sperm principal pieces.
mRNA expression analysis of lipoprotein receptors in HUVECs. Data presented as mean ± StDev relative to RPL19 expression from 3 independent experiments.
A Schematic representation of the UbG76V-GFP chimeric reporter (yellow for ubiquitin and green for GFP) and its associated mRFP internal control (red). The UbG76V-GFP chimera, which contains a mutation in the terminal residue of ubiquitin, cannot be cleaved. The resulting protein is a substrate for poly-ubiquitination (indicated by the circles labeled with "u") and degradation by the proteasome. High levels of reporter poly-ubiquitination and/or proteasome activity result in little or no GFP fluorescence.
Quantification of colocalization of vDNA foci detected by click chemistry to PML in primary SCG neurons transduced with shRNA targeting PML at 1 day post-infection with HSV-1EdC in the presence or absence of IFNα (150 IU/ml). Each point represents the percentage of 20 vDNA foci that colocalized to PML from 3 biological replicates.
(G) Maximal intensity projection of a confocal z-stack of MZsinhcaf -/- or WT 4-cell stage embryos injected with GFP-Buc mRNA + RFP mRNA or GFP-Buc mRNA + RFP mRNA + kif26ab mRNA. White arrowheads point to cleavage furrows of 4-cell embryos.
(C) Boxplots of the transcription levels of the 87 most highly transcribed SAGA- and TFIID-dependent genes as determined by NET-seq. Significance was assessed by t-test.
EC-miR-483-Tg rats and WT littermates were injected with SU5416 and then exposed to hypoxia for 3 weeks and had reoxygenation for 2 weeks or injected with DMSO and exposed to normoxia for 5 weeks. Analysis of mPAP (E) for the indicated groups. Data information: Values are expressed as mean ± SEM. Statistical test: t-test (*P < 0.05 vs. respective controls or between the indicated groups).
(H,I) Shh levels assayed by ELISA in the medium of slices (H, n=9) or hippocampal neurons (I, n=6) incubated with picrotoxin (Pic) or Mg2+-free (0Mg) for the indicated times.
Translocation intermediates (IM) were incubated in the presence of different nucleotides (Nuc.) for different time periods and then treated with proteinase K (Prot. K). One sample received hexokinase and glucose (HKG) to generate ADP, other samples ADP•BeFx or ATPγS. The gel is representative of two replicates.   Quantification of (C). Points show IM band intensities normalized to the 0-min time point for each replicate. Lines show the average of replicates. Colors correspond to different nucleotides as shown in the inset box.   As in (C), but DTT was added concurrently with HKG or nucleotides. The gel is representative of two replicates.   Quantification of (E) as in (D), except intensities were calculated for the FL bands.
A Schematic diagram showing the domain structure of human Ykt6 protein. Ykt6 has two cysteine residues, Cys194 and Cys195, at the fifth and fourth positions from the C-terminus.
C, D ChIP-qPCR analysis of Pol2 association with early replication origin ARS305 or ARS607. HA-tagged Pol2 interaction with chromatin was monitored in wild type (TB067) and scc2-4 (TB068) cells. Error bars represent mean value ± standard deviations of mean (n=3)
(A) atg1Δatg13Δ cells containing an empty control plasmid, wild‐type or the indicated Atg1 mutants, and Atg13 wild‐type, the Atg13‐FVmutant or an empty plasmid were grown to mid log phase. Processing of endogenous Ape1 was analysed by western blotting, and quantified as described in the legend of Figure 1I. Expression of the different proteins was controlled by immunoblotting with antibodies against Atg1 or Atg13. The asterisk marks a non‐specific band detected by the Atg13 antibody.
Plating efficiency of ex vivo cultured E18.5 small intestines quantified 6 days after initial seeding. Each symbol indicates the value for a given embryo.
A. DNA unwinding by DnaB was initiated from the upstream side of the PAM in the presence of dSaCas9 (n = 10). Representative traces show the number of unwound base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9. For clarity, the traces have been shifted along the time axis. The dashed lines indicate the expected dSaCas9 binding positions. B. DNA unwinding by DnaB was initiated from the downstream side of the PAM in the presence of dSaCas9 (n = 11). Representative traces show the number of unwound base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9. C. DNA unwinding by BLM was initiated from the upstream side of the PAM in the presence of dSaCas9 (n = 12). Representative traces show the number of unwound base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9. D. DNA unwinding by BLM was initiated from the downstream side of the PAM in the presence of dSaCas9 (n = 14). Representative traces show the number of unwound base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9. E. Phi29 DNAP strand-displacement synthesis was initiated from the upstream side of the PAM (n = 15). Representative traces show the number of unwound/synthesized base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9. F. Phi29 DNAP strand-displacement synthesis was initiated from the downstream side of the PAM (n = 19). Representative traces show the number of unwound/synthesized base pairs versus the time under an assisting force of 12 pN in the absence (black) or presence (red) of the prebound dSaCas9.
B. Representative inward current traces elicited by 100μM D-Asp application in MO3.13 cells in the absence or in the presence of 10μM DNQX
(C) Absolute bacterial counts (CFUs) in human THP1 macrophages 1 h after infection with MTB pre-incubated with the LAM-reactive IgA1 (left) or IgG1 (right) antibody TB24PB037 or the respective isotype control antibody as indicated. Mean and SEM are indicated.
(C) Co-immunoprecipitation and immunoblot analysis of extracts of Flag-NS1-inducible THP-1 cells treated with or without Dox (100 ng/ml) then transfected with or without poly (I:C) (2 mg/ml, 6 hrs).
(E) Top: PAGE gel showing a representative unwinding assays in which purified MBP-DDX5-GST (1-5 nM) was incubated with 32P-labelled synthetic R-loop substrate in presence or absence of 50 nM purified BRCA2T1-T207A (bottom right). Bottom left: Quantification of the unwinding experiments showing the percentage of free RNA relative to the R-loop substrate (unwound product) as a function of DDX5 concentration alone (black) or in presence of BRCA2T1-T207A (green). The data represent the mean ± SD of at least three independent experiments. Bottom right: SDS-PAGE showing 650 ng of purified 2XMBP-BRCA2T1-T207A used in the unwinding assay.
Volcano plot of ERα dependent miRNA expression in BM67 cells quantified by small RNAseq. Down- and up-regulated miRNAs (FDR<0.2 and fold-change > 1.25) are colored in blue and red, respectively.
Separase interacts with γH2AX in DSB-containing G2 but not G1 cells. Transgenic Hek293 cells treated with Dox to induce expression of Myc-separase-WT and with OHT to induce nuclear accumulation of ER-AsiSI and infliction of DSBs were synchronized in G1- or G2-phase and analysed b IFM for γH2AX- and Myc-separase-positive foc The quantification of the IFM in (E) shows averages (bars) of 3 independent experiments (dots) counting ≥ 100 cells each
A) log2(H/M) values for 5 synaptic proteins for which degradation rates were significantly slowed down in the presence of lactacystin. Each point represents average log2(H/M) from 3 experiments. B) log2(H/M) values for the same 5 synaptic proteins in experiments in which epoxomicin was used. Each point represents average log2(H/M) from 2 experiments. C) Average (± SEM) log2(H/M) ratios for the same 5 synaptic proteins, based on all five experiments (3 lactacystin, 2 epoxomicin). P values - two-tailed Welch's t-test, comparing the five log2(H/M) measurements at t=24 to those measured for the same proteins at t=0.
dHepG2H1.3 cells were treated for one day with 1000 U/ml IFNγ and harvested proteins were subjected to an affinity purification-mass spectrometry assay (n=4 technical replicates). Oligomers used for pulldown were single-stranded or double-stranded DNA with and without dU as indicated.
(A) Transcription at GAL3 is visualized by addition of PP7 loops at the 5' of GAL3 in budding yeast. Example trace of the quantified fluorescence intensity of the transcription site. Traces are binarized to determine on (active) and off (inactive) times.
CHX chase assay (100µg/ml) of control or inducible mUSP28 overexpressing A-431 cell line (EtOH or 1µg/ml dox) for indicated time points. Representative immunoblot analysis of USP28 and ∆Np63 as well quantification of relative protein abundance (VINCULIN as loading control).
C. Replication timing programme is intact in rif1-∆C594 cells. Replication of selected origins at an HU block analysed by BrdU incorporation. Cells were synchronised by α-factor and released into the medium containing 0.2 M HU and 1.13 mM BrdU. Plots show the percentage of total ARS607, ARS422.5, or ARS1412 DNA pulled down by IP with anti-BrdU, calculated from two biological replicate samples. Bars indicate the average of two biological replicates and open circles the values from each replicate. Insets in ARS422,5 and ARS1412 panels show the same data with Y-axis scales adjusted to 0 - 0.03%
Oct4-eGFP reporter MEFs or WT MEFs were infected with a vector expressing the indicated shRNA in combination with the indicated cDNA (OE indicates overexpression), Cells were co-infected with 4 reprogramming factors (4F= Oct4, Sox2, Klf4, c-myc = OSKM) and double-infected cells were FACS sorted for analysis. (A) RT-qPCR analysis on day-4 after infection to determine RNA expression of Tnfaip2 or Vim in Tnfaip2-depleted cells with ectopic expression of Vim (left) or in Vim-depleted cells with ectopic expression of Tnfaip2 (right). Scramble shRNA (shScr)-infected MEFs served as a control [n=3 biological replicates; log-transformed data were normally distributed (P>0.05 as per Shapiro-Wilk test) and analyzed by t-test].
B. Schematic representation of the simulation process used to probe the stability of longitudinal and transverse patterns. The system is initialized with a homogeneous configuration and the gradient of the MinD attachment rate is aligned with the major or minor axis to direct pattern selection. After initialization the MinD attachment rate is equalized to allow the system to relax into the initialized state. If the initialized pattern persists in the absence of a stabilizing gradient, the gradient is reapplied to deflect the pattern from its preset alignment and study its stability vis-a-vis spatial inhomogeneities that break its symmetry. The stability towards all possible deflections with linear MinD attachment profiles is probed and the persistence of the initialized pattern is checked.
G. Endogenous MITOL enhances the K48-polyubiquitin chains of Parkin. WT or MITOL KO HeLa cells stably expressing HA-Parkin were treated with CCCP (10 µM) for indicated time. MG132 (30 μM) was added 3 h after CCCP treatment. Lysates of cells were fractionated into cytosolic, mitochondrial and ER fractions, and then subjected to an IP-IB assay with the indicated antibodies. K48-polyubiquitin chains were immunoblotted with K48-specific ubiquitin antibody.
A The structure of full-length PrP and derivative C1 and C2 fragments with an enlarged view of the cleavage sites is shown. The C2 (β) site was mapped in HpL3-4 cells by (Mange et al, 2004). Ragged C1 (α) cleavage sites in brain are shown (Chen et al, 1995), and a dotted arrow indicates that additional sites have been mapped rightward of this position in vitro (McDonald et al, 2014). Ragged N-terminal cleavage sites of PrP27-30 from prion-infected mousebrain are indicated by small arrows (Howells et al, 2008). The positions of antibody epitopes are also shown (residues in brackets). Grey shading reflects the minimum length for a C2 fragment defined operationally by reactivity with 12B2 antibody.
Sublingual infection of WT, Stim1fl/flVav-iCre and Stim1fl/flStim2fl/flVav-iCre mice with 2x107 CFU of C. albicans. (A) Body weight (BW) measured for 7 days and normalized to BW at day 0 of infection. Data are mean ± SEM measured from 4 repeat experiments and 13 WT, 7 Stim1fl/flVav-iCre, 8 Stim1fl/flStim2fl/flVav-iCre mice.
(G) HeLa cells were lipofected with a cDNA encoding for GFP-DYRK3. 16 hrs post-transfection, cells were incubated for an additional 8 hrs in drug-free medium (-) or in presence of GA or 17AAG alone or combined with MG132 (concentrations are shown). Total proteins were extracted and GFP, ubiquitin and TUBA4A protein levels were analyzed by immunoblotting. Representative immunoblotting of 3 independent experiments.
R. Percentage of normal, abnormal and missing rhabdomeres in ADAM17-/- mutant retinas, as compared to retinas overexpressing glial specific SOD2 in an ADAM17-/- mutant background observed with TEM; n=180 ommatidia from 3 different fly retinas for each.
B IFNAR1 mRNA stability after DRB treatment. 293T cells were transfected with RBM47-Flag or empty vectors and treated with DRB (50 μg/mL). Total RNA was harvested at 0, 15, 30, 45, and 60 min, and IFNAR1 mRNA levels were measured using qRT-PCR and normalized to β-actin. The PCR results are represented as the means ± SD of n = 3 biological replicates. Data information: Data are representative of n = 3 independent experiments. NS, non-significant; **P ≤ 0.01, and ***P ≤ 0.001 (Student's t-test).
M Relative mRNA expression levels of EMT‐related marker genes upon Sox2 depletion in KPNC tumor cells (P 0.05).
E. Schematic of how candidate phosphorylation sites were narrowed down to 179 secretion connected phosphopeptides.
(D Depletion of ATP5ME in HeLa cells. Cells were transfected with a scrambled control or siRNA pools against ATP5ME for 4 d. TEM recording (left) and quantification of the number of cristae per mitochondrial section (right).
Quantification of relative mean fluorescence intensities (MFI) between empty vector and Siglec-expressing populations. Relative values are shown for each mouse and human Siglec construct for uptake of monomeric Aβ, Bars indicate mean ± 95% CI; n = 6 replicates; *: p < 5e-2, **: p < 1e-2, ***: p < 1e-3, ****: p < 1e-4; ns: not significant, using unpaired Student's t-test, two-sided. Dotted line indicates mean of 2xY->F group.
The cartoon summarizes the localization of hCDC14A on cilia. The distal appendage protein CEP164 marks the mother basal body. The C-Nap1 organized centrosome linker connects the mother with the daughter basal body (black lines). ODF2 and ninein mark the subdistal appendages. Note, ninein has a second localization at the distal end of basal bodies. hCDC14A localized to the subdistal appendages and the C-Nap1 marked proximal end of the basal bodies
(C) Gene deletion and G0 phase synchronization protocol for mouse embryonic fibroblasts isolated from Cdca5 flx/flx mice expressing ERT2-Cre.
C. Example of dissected brains (upper panel) and coronal sections (left and right panels) stained with H&amp;amp;E of the indicated genotypes. Note the severe hydrocephaly and ventricular dilation of the lateral ventricle (LV) and third ventricle (TV) in a Gemc1-/- mouse (bottom right panel) compared to a Gemc1+/+ littermate animal (bottom left panel). Periventricular malacia (asterisks) and hippocampal atrophy (arrow) is also evident in the Gemc1-/- sample. Scale bars = 500 µm.
Western blot of conditioned media (CM) of transduced fibroblasts showing mature activin βA. Ponceau S staining of the membrane was used as a loading control.
B. Representative primary data - polyacrylamide gel (the experiment was performed 3x with the same results). Lane 1, the full length (33 nt) labeled RNA; lane 2, the same as lane 1 but it included also incubation with RNase J1 (J1), 17-18 nt long fragments (RNase J1 stopped by RNAP; indicated with asterisks) and <5 nt fragments (RNA released from TC into buffer - indicative of TC disassembly) are shown; lane 3, the same as lane 1 but included also incubation with RNase R (R); lanes 4 and 5, TCs were denatured by heat prior to RNase addition to demonstrate the activity and cleavage patterns of both enzymes; lanes 6 and 7, the same as lanes 2 and 3 but the buffer was washed off (TCs were retained by streptavidin beads) to demonstrate which RNA fragments were associated with TC; lanes 8, 9 (M1, M2) Mw marker generated by treating the 30 nt RNA with alkali and formamide (M1-4 min treatment, M2-7 min treatment). As reported in (Costanzo et al., 2016) [and references therein], the cleavage by alkali or formamide leaves the phosphate group of the attacked phosphodiester bond bound at 3', initially in the 2',3' cyclic form (upper band in the band couples). This successively opens (lower band in the band couples) yielding a double-banded pattern for short oligoribonucleotides.
b, THP1 cells expressing Flag-NLRP3 were analysed for the co-localization of Flag-NLRP3 with the endoplasmic reticulum (ER) marker calreticulin using confocal microscopy.
Co-immunoprecipitation between endogenous β-catenin and UBTD1 was performed in confluent DU145 cells. IgG isotype was used as a negative control.
(A) Schematic of (CGG) 90-EGFP construct and experimental outline for rough eye phenotype screening.