EMBO/sd-character-level-ner huggingface dataset:
Dmxl1 was knocked down in WT iBMDMs or Tpl2[D270A] iBMDMs by RNA interference using a SMARTpool ON-TARGETplus siRNA for 48 h. ON-TARGETplus non-targeting pool functioned as siRNA control. (D) Intra-phagosomal acidification was assayed following uptake of BCECF-coupled latex beads by WT iBMDMs. As a control, BMDMs were pre-treated with 1 μM bafilomycin A1 for 15 min to directly block V-ATPase function (n = 4 wells). (E) Intra-phagosomal acidification was assayed following uptake of BCECF-coupled latex beads by Tpl2[D270A] iBMDMs (n = 4 wells). Data Information: One representative experiment out of three shown. Error bars and shaded areas represent SEM. **** P < 0.0001. Paired Mann-Whitney t-test. All differences relative to WT are ****. US, unstimulated; UT, untransfected; NT, non-targeting siRNA pool.
(a) Increased expression of TEs in stem cells of D7 seedlings according to qRT-PCR. Box plots outline the interquartile range (IQR) with the median and whiskers +/- 1.5 IQR. N = 2 (ATLANTYS3, ATCOPIA39, ATCOPIA49, ATCOPIA29, ATGP1-1), N = 3 (VANDAL6, ATGP2, ATGP1-2, ATLINE1, ATGP1-3), N = 4 (ATHILA6A, ATCOPIA83), N = 5 (VANDAL12, ATHILA3, ATCOPIA22), and N = 6 for CLAVATA. *p<0.01, **p<0.001 (t-test).
A) ykt6ts pho8∆60 cells containing an empty plasmid, GFP-Ykt6 or 3HA-Ykt6 on a centromeric plasmid and pho8∆60 cells containing an empty plasmid were grown at permissive temperature (23 ºC) to late exponential phase in selective medium. Cells were shifted to the restrictive temperature (37 °C) for 1 hour (light grey bars) and subsequently starved for 4 hours in SD-N medium at restrictive temperature (black bars). Pho8Δ60 alkaline phosphatase activity was measured in three independent biological experiments and the mean was plotted normalized to starved Pho8Δ60 alkaline phosphatase activity. Error bars represent the standard deviation.
D. BAZ2A is required for the dedifferentiation of PC3 into PC3-CSCs. Left panel: Representative images from two independent experiments showing the impairment of PC3 cells to form tumorspheres upon stable depletion of BAZ2A. Right panel: BAZ2A mRNA levels in three independent PC3 cell lines stably expressing shRNA-BAZ2A were measured by qRT-PCR and normalized to GAPDH mRNA from 2 independent experiments.
esgts midguts expressing GFP alone (control), or expressing pri-RNAi, and quantification of GFP-positive cells (green). The graph also shows the number of YFP-positive cells in ISCts midguts expressing YFP alone (ctrl), or pri-RNAi (see EV2A).
C. IL-10 mRNA levels, determined by RNA-sequencing, in TCRβ+ CD4+ cells purified from spleens of L. donovani infected WT (blue) or miR-132-/- (red) mice (n=5 per group).
D. Quantitative RT-PCR analysis of RNA isolated from mouse liver for FoxM1B, Birc5 and cyclin B1 at 0 and 40 h post PH. Log2 fold change was calculated using non-transfected/non-resected mouse liver as a control. Representative results of a single experiment with n = 6 animals per group are shown. Paired, two-tailed Student t-test was used to calculate the significant change in signals between liver tissues at the time of resection (0h) compared to 40 h post PH.
B. Quantification of in vitro matrigel invasion assay (bottom) of P-NF and L-NF and P-CAF#110 and L-CAF#400 transfected with control or hMENA∆v6 expressing vectors, demonstrating that the overexpression of hMENA∆v6 isoform induced the invasiveness of P-NFs and L-NFs and/or P-and L-CAFs. Number of invading cells was measured by counting 6 random fields. Data are presented as the mean ± SD of two biological replicates, performed in triplicates each. Immunoblot of hMENAΔv6 expression (detected by the specific anti-hMENAΔv6 antibody) in fibroblasts employed is reported (top). TUBULIN was used as loading control. P values were calculated by two‐sided Student's t‐test. *P<0.05, ***P<0.001.
(F) Effect of ND-011992 on the OCR of M. smegmatis IMVs using the Oroboros O2k fluorespirometer. IMVs OCR from the parental strain (green triangles), ∆cydAB knockout (blue circles), and ∆cydAB complemented with M. tuberculosis CydABDC+ (red squares) energized with NADH were determined. Q203 was used at 1 μM. 100% OCR was defined as the OCR of the untreated samples for each strain.
b, Representative confocal images of endogenous OFD1 and acetylated tubulin in Atg5+/+ and Atg5−/− MEFs subjected to 24 hserum starvation. a, b, Data shown represent mean ± s.d. percentage of cells with centriolar satelliteOFD1 for 100 cells per well in triplicate samples. ***P 0.001, two-tailed unpaired student's t-test. Similar results were observed in three independent experiments.
A-H Effect of CCCP on the localisation of Noc and NocNΔ10. Cellular localisation of Noc‐mYFP (DWA206) and NocNΔ10‐mYFP (DWA382) either with no additions (NA) or after CCCP treatment (5 min; 100 μM), as indicated. Scale bar, 2.5 μm.
C Co-immunoprecipitation of endogenous PTAR1 and RabGGTβ from rat brain and thymus cytosol.
C. T6SS secretion assay of A. tumefaciens C58ΔG2op mutant encoding full-length or truncated VgrG1 proteins.
CFU-C numbers in Tie2Cre::Kitl∆/∆ and control Kitlf/f or f/+ E11.5 Fl. Data are the mean (±SD) of 7 control and 5 Tie2Cre::Kitl∆/∆ FL plated in duplicate in 3 independent experiments. GEMM: granulocyte, erythroid, monocyte/ macrophage, megakaryocyte; G/M/GM: granulocyte, monocyte/macrophage; Ery: erythroid. Tail somite range: 13-16.
(B) LN229 cells treated with DMSO, ionomycin (Iono) or thapsigargin (TG) were lysed 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.
(C) A table showing the expression status of Gpr56 WT and S4 variants in microglia of different transgenic mice.
Steady state levels of NDUFB10, NDUFS5, NDUFA8, COA6, CHCHD2, and TIMM9 upon incubation with the DPP9 inhibitor 1G244. Cells were treated for 24h with inhibitor or DMSO as control, and were then analysed by immunoblot against the indicated proteins. Proteins except TIMM9 are stabilized upon DPP9 inhibition. Reported values are the mean of 3-5 independent experiments; error bars represent ±SD. Student's t-test was performed. ** represents p<0.01.
(g) Flow cytometry of untreated macrophages (control) or of macrophages stimulated with LPS and ATP, stained with MitoTracker Deep Red. Numbers above bracketed lines indicate percent cells with loss of mitochondrial membrane potential.
(C) High magnification of a single confocal cross-section of wild-type and Snap29 mutant eye disc tissues. Two facing folds of the tissue are separated by the apical lumen. aPKC and Dlg mark the apical and lateral plasma membrane domains, respectively. In Snap29 mutant tissue the apical-basal polarity is disrupted.
Detection of synthetic SARS-CoV-2 RNA using commercially available paper strips (lateral-flow) in saliva (C).
(B) Left panel: immunoblot analysis of total PDH protein levels and the inactive phosphorylated (repressed form), PDHS293, in control (C1, C3), WHS LETM1+/- (S1, S3, S4) and WHS LETM1+/+ (S5) fibroblasts. Center and Right panels: Immunoblot analysis of PDK3 in control (C1-C3), WHS LETM1+/- (S1, S3 and S4) and WHS LETM1+/+ (S5) fibroblasts
ORP3+/+ and ORP3−/− hTERT-RPE1 cells incubated for 24 h without serum were immunostained with anti-pericentrin (red) and anti-acetylated tubulin (blue) antibodies. Cholesterol was stained with Filipin III (green). Arrows indicate primary cilia. Scale bar, 5 μm. Quantification of the Filipin III intensity at primary cilia from (C). ORP3−/− hTERT-RPE1 cells exhibited a significant reduction of ciliary cholesterol (***p<0.001: one-way ANOVA with Tukey's HSD, n=3: 40-50 cells per experiment). In the boxplot, medians, 25th/75th percentile and min/max were represented by the central lines, the box limits, and the whiskers/error bars, representatively.
(A) The E406-R479 (GltPh Q318, R397) salt bridge locks HP2 in the open state in EAAT1. Image shows the region around residues 406 and 479 (shown as spheres) with HP2 open (gray cartoon). Both residues sterically prevent HP2 closure by forming a salt bridge.
Quantifications of VPS16 in fibroblast lysates by immunoblotting. Representative immunoblots (bottom) and summary quantifications (top) of the levels of VPS16 in patient A (n=4) and patient B (n=3), normalized to levels of actin (ACTB) and expressed as % of controls.
Genes enriched for gene‐trap insertions in a carboplatin‐selected cell population compared to unselected control cells. Circles represent genes and their size corresponds to the number of independent insertions identified in the carboplatin‐selected population. Genes are ranked on the x‐axis based on chromosomal position.Location of gene‐trap insertion sites (red arrowheads). White boxes indicate the 5′‐ and 3′‐untranslated regions, and the black boxes show the coding sequence in exons 3 and 4 (LRRC8A) and exon 3 (LRRC8D).
F. Western blot analysis of samples from independent small-scale streptavidin purifications (termed 'Eluates') following the proximity labeling approach outlined in (B). The indicated proteins were detected with specific antibodies. M indicates the marker lane. Data are representative of at least two biological replicates.
D Representative transmission electron microscopy images of FACS-sorted human CD3+MitoTneg and CD3+MitoTpos cells following mitoception with UC-MSC MT. Red arrows show human mitochondria.
G The resident/intruder experiment showed that the attack duration (G) of the miR-200b/a KD mice were impaired compared to those of the NC mice (NC: n=11 mice, miR-200b/a KD: n=10 mice; data represent the mean±SEM; ****p<0.0001; Student's t-test).
(C) WT or Atg16L1Δ/Δ MEFs in fed medium or starved for 2 hr in EBSS were fixed and labeled with an anti-WIPI2 antibody. Scale bars, 10 μm.(D) WIPI2 puncta in (C) were counted, and a statistical analysis of WIPI2 puncta was performed using an unpaired Student's t test. ∗p < 0.05. SEM for n = 3.
(C) The excision of IS3 family transposase has created operonic fusion of TA and T6SS related genes. Moreover, a new ORF of 474 bp that encode a H.P (hypothetical protein) has evolved at the locus, through adoption of 3' end of the DUF4123 and 5' end of the toxin gene.
(F) LM2 cells transfected with siRNA targeting PTPRN2, PLCβ1, or control siRNA were partially permeabilized and incubated with biotin-actin monomers. Cells were stained for incorporated biotin-actin monomers using Streptavidin-555 (red) and DAPI (blue). Right, quantification of mean fluorescence intensity of incorporated biotin-actin monomers. N = 100 cells/group. Scale bar, 20 μm.
Representative confocal images of Cav1 staining in heart sections from control and RbpjiΔEC mice. n=3, scale bar 50 µm.
Length distribution of chromatin-bound and nucleoplasmic piRNA precursors in wild type N2 nematodes, calculated from two merged replicates.
G, J Impact of TRAF6-expression on in vitro Treg differentiation. naïve CD4+ T cells were isolated from Traf6fl/flFoxp3Cre+ and Traf6fl/fl mice and differentiated into iTregs. Conditions of sub-optimal TGFβ concentrations (0.5ng/ml, 0.05ng/ml) were tested as well and intracellular FOXP3 was measured after 4 days.
D. Schematic representation visualizing the hGID E3 ligase complex using two distinct modules for substrate recruitment.
Relative intracellular Fe2+ levels in normoxic B16-F10 cells (n=4). Representative pictures of FerroOrange intensity are shown on the left and analyzed using a RM one-way ANOVA (Geisser-Greenhouse correction) with Holm-Sidak's multiple comparisons test. Scale bars represent 50µm.
(C Small RNA and Poly(A)-selected RNA sequencing based estimates of the fold difference (y-axis) in (C) miRNA relative to day 0, during a 12 days' time-course (x-axis) following treatment of DTCM23/49XY mESCs with 4-OHT and consequent loss of DICER function. Points represent the average miRNA or mRNA expression and error bars the standard deviation based on three independent biological replicates.
C: The pie chart depicts the percentage of patients of the PDAC cohort (n=75) belonging to the three PRMT1 expression scores: not elevated, moderately elevated and highly elevated PRMT1 expression.
A. Representative confocal microscopy images of cells transfected GFP-LC3 and Parkin-Cherry, treated as indicated, fixed 24h after AICD induction and immunostained with anti-TOM20 antibody are shown. Scale bar, 5μm.
I) Synaptic surface GluA quantitation showing no effect of PTX3 treatment in TSG6 KO cultures. On the contrary WT cultures (from littermates) display increased surface GluA&Bsn/Bsn upon PTX3 treatment. A significant enhancement of surface GluA receptors was induced by TTX in both TSG6 KO and WT cultures (WT=1±0.06; WT+PTX3=1.389±0.113; WT+TTX=1.698±0.109; Number of fields examined: 40, 39, 32 respectively; Kruskall-Wallis test p<0.0001 followed by post hoc Dunn"s test. TSG6 KO=1.000±0.047; TSG6 KO+PTX3=0.979±0.048; TSG6 KO+TTX=1.363±0.077. Number of fields examined: 54, 57, 29 respectively; one-way ANOVA analysis of variance, p<0.0001 followed by post hoc Tukey test as indicated in figure. n=3 independent experiments, data are presented as normalized mean values
B Immunoblotting of protein extracts from SKMEL5 cells transfected with siCTRL or the combination siDDR1#2/siDDR2#2 prior being cultivated on FRC- or MAF-derived ECMs (left and right panels, respectively) and treated with vehicle, 5 µM BRAFi or 2 µM BRAFi plus 0.01 µM MEKi, using antibodies against the indicated proteins. HSP60, loading control.
A, B Nucleosome maps at and surrounding, the TSS region of the NANOG and GRIA1 genes in pl-iPSC (upper, black) and in NPC cells (lower, grey). The TSS is indicated by a dashed line at chr 12: 7,941,991 for NANOG and chr5: 152,870,105 for GRIA1. * indicates the position of a highly positioned nucleosome associated with the TSS of the active gene.
A, Western blot analysis of 293T cells treated with 20 μM erastin for the indicated times.
(D) Control and GRASP55KO cells were processed for Cy3-conjugated Shiga Toxin (ShTxB) and Alexa488-conjugated Cholera Toxin (ChTxB) staining followed by flow cytometry analysis. Mean fluorescence intensity was measured and represented.
G Schema of experimental design. H2030-BrM cells were implanted intracranially into nude mice and established brain metastases were surgically resected. DEBIO-0932 was administered orally at 160 mg/kg 3 days later and during 5-6 weeks following an individualized regimen. Sx: surgery.
D HeLa cells were treated with control or siRNA targeting ALFY. 72 h after transfection, cells were treated with puromycin with or without bafilomycin A1 for 2 h and total cell lysates were fractionated into TX−100−soluble and insoluble fractions. The TX−100−soluble/insoluble fractions were then immunoblotted with the indicated antibodies. Data are representative of three independent experiments.
(B-D) Representative single channel traces and summary plot upon depolarization from -80 to 0 mV under control conditions and in the presence of ISO in the patch pipette. Cultures were pre-incubated for 15 min with 10 M 11R-PKI if indicated. The patch pipette contained either vehicle for control, nifedipine (nif; 1M), ISO (1M), or ISO plus nifedipine, which blocked all currents. The ISO-induced increase in NPo was prevented by 11R-PKI.
A-C Representative images shown for olive oil treated (n=5) or chronic CCl4 (n=5) induced fibrosis or following sham operation (n=6 Sox9fl/fl;AlbCre-; n=5 Sox9fl/fl;AlbCre+) or BDL (n=5 Sox9fl/fl;AlbCre-; n=8 Sox9fl/fl;AlbCre+) induced fibrosis. SOX9 immunohistochemistry (brown; A), in situ hybridization for Sox9 (brown) and α-Sma (red) and collagen deposition by PSR staining (red; B) in control (Sox9fl/fl;AlbCre-) or Sox9-null (Sox9fl/fl;AlbCre+) mice following fibrosis. Higher magnified image of SOX9 localization in discrete cells within the scar is shown for CCl4 and BDL in the Sox9fl/fl;AlbCre+ mice (A).
(E) Immunoblot analysis of the BioID assay with an N-terminally Flag BirA*-tagged SLC25A46 showing an interaction of SLC25A46 with EMC1, EMC2 and MFN2.
D-F Two‐month‐old APC+/+ mice and APCmin/+ mice were exposed to 6 Gy γ‐irradiation. Small intestinal tissue was collected at 24 h after IR (n = 3 mice per group). (D) Quantification of PCNA+ ISPCs at the indicated positions in basal crypts 24 h after IR. IR, irradiated. (E, F) Representative pictures of PCNA staining are given. Arrowheads and numbers indicate cell positions in the crypts. Scale bar: 20 μm.
(J-L) Cumulative population doublings of patient-derived KRAS-mutant LUAD cell lines that are either (J, K) NF1-mutant (PDKN1 and PDKN2) or (L) NF1-WT (PDK) after selection with sgTom- or sgPsat1-containing vectors (n = 4 biological replicates).
(A) Western blot analysis showing the expression of the WRNIP1 protein in wild-type cells (shWRNIP1WT) and WRNIP1-deficient (shWRNIP1) or mutant (shWRNIP1T294A) cells. MRC5SV fibroblasts were used as a positive control. The membrane was probed with an anti-FLAG or anti-WRNIP1. GAPDH was used as a loading control. Below each lane of the blot the ratio of WRNIP1 protein to total protein, then normalised to MRC5SV, is reported.
I Alignment of the genomic region 1.5 Kb upstream of the mammalian Sln gene using the ECR Browser (http://ecrbrowser.dcode.org/). Human was used as the reference genome. The location of conserved NFAT binding sites are indicated by blue diamonds and CREB sites by yellow. Sites were conserved across all mammalian species available in the database except opossum. Mouse, rat, and dog are provided as representative examples. The structure of the Sln-Luc reporter construct is aligned below.
A. Schematic representation of the domain structure of Nmd4 and Ebs1 from S. cerevisiae compared with human (h) Smg6, Smg5 and Smg7. 14-3-3, HHR and PIN domains were defined based on literature data (Fukuhara et al, 2005; Luke et al, 2007). Boundaries of the PIN domains were chosen based on a Mafft alignment of Smg5/6 of several species, while for Nmd4 the entire protein sequence was used. Drawing is not to scale. Identity percentages among the different domains of Smg proteins, Nmd4 and Ebs1 are indicated. Values represent percent of identical residues as a fraction of all the aligned residues
H&E images of paraffin-embedded liver sections from 9-week-old mice (n=4 per group, 3 independent repeats).
Combined IF and DNA FISH for RAD51 (IF) and telomeres (FISH) in SaOS2 or HuO9 cells. Cells were transfected with 20nM siRAD54#2 for 48 hours immediately prior to staining. Scale bars = 10 µm Quantification of A. A cell was counted as positive it is contained at least 1 colocalization event between RAD51 and telomeres. At least 100 cells were counted per condition per repeat, n=3. Values shown are mean±sd. Data were compared using standard two-way ANOVA followed by Sidak's multiple comparison test.
(B) Coomassie-stained SDS PAGE gel showing proteins immunoprecipitated from schizonts expressing SERA6-mTAP, sampled at the indicated times following C2 washout or arrested with E64 (50 μM). Control, proteins immunoprecipitated from SERA6:loxP (Thomas et al, 2018) schizonts, which express non-epitope-tagged SERA6, sampled at 5 min following C2 washout. Arrowed, species analysed by mass spectrometric peptide mapping. Fragments A-H were identified as SERA6-mTAP-derived, while fragments I and J were derived from a different protein, PF3D7_1014100.
Longitudinal associations between CSF T-tau, Ng and NFL and other AD traits. Data are estimates (-coefficients) from linear mixed effects models, with 95 % confidence intervals. The estimates are the effect of time plus the biomarker by time interactions, capturing the longitudinal effects of the biomarkers. For each model, the "average" effect of time is also shown for comparison. Effects were significant (*), meaning that biomarker levels affected the slopes of the outcome, for lateral ventricles: Ng (p=.0051) and NFL (p<.0001) in A-negative and NFL (p<.0001) in A-positive. Biomarkers and outcomes were standardized to z-scores. Note that the y-axes for ventricle size are flipped, so that the lower ranges constantly reflect "worse" outcomes. Note also that the range of the y-axes differs for the different outcomes, for visualization purposes. Models were adjusted for age and sex, and education (for cognitive measures), and intracranial volume (for MRI measures). Aβ42 and T-tau were measured using the the INNOBIA AlzBio3 kit (Fujirebio, Ghent, Belgium), Ng was measured using an in-house immunoassay for Ng (Portelius et al, 2015) and NFL was measured using the NF-light® ELISA kit (Uman Diagnostics, Umeå, Sweden).
(C) Quantification of normalized MA current amplitudes from DRG neurons, vehicle (white, n=7), neurons responding to baclofen (R, red) (n=6, **P<0.01, Paired t-test and non-responding DRG neurons (NR, blue, n=6). Striped column shows the average normalized current amplitudes 3-10 minutes after removal of baclofen in responding neurons (Washout) (n=6). Data are shown as mean ± SEM and scatter plots.
(G) IRE1 cleavage assay performed using synthetic pre-miR-2137 (50 nM) as substrate with active, recombinant IRE1 (100 ng) at 37℃ for 2 hours, followed by sample separation in Urea-PAGE and detection with SYBR gold staining. M indicates micro RNA marker.
Schematic representation of the novel TRF1 regulatory pathways. Data are represented as mean ± SEM. n represents biological replicates. Significant differences using unpaired t‐test are indicated by *P < 0.05, **P < 0.01, ***P < 0.001.
(F, G) Indicated promoter activation was analyzed with luciferase assay. DKK1 was used as a control. Results of relative fold changes are shown as means ± S.D. Data represent five independent replicates. . ** p<0.01 by two-tailed Student's t-test. .
(G) Samples from an analogous experiment to that shown in (F) were analysed by immunoblotting of the indicated factors. The asterisk indicates a non-specific band in the immunoblot for histone H2B.
Wnt inhibition using siRNA against β-catenin or ETC-159 treatment reduces the expression of HR and FA pathway genes in PaTu8988T cells. PaTu8988T cells were transfected with indicated control or β-catenin siRNAs or treated with ETC-159 (1 µM) for 48 hours, total RNA was isolated and expression of β-catenin (CTNNB1), AXIN2 and DNA repair genes was measured by qRT-PCR. The horizontal lines represent mean of replicates.
(a) MSCV retroviral constructs introduced in P14 cells (Supplementary Fig. 2a) to probe for autophagy activity, showing the transgenes encoding GFP-tagged wild-type LC3b (top; WT GFP-LC3b) and the GFP-tagged G120A mutant of LC3b (bottom; G120A GFP-LC3b). LTR, long terminal repeat; IRES, internal ribosomal entry site.
(J) Y245F mutant induced more LC3 lipidation after 1h cGAMP treatment of 293XL cells expressing WT or mutant STING.
H Diffusion coefficient of lysosome in the experiments shown in G. Means ± SEM of n = 4 cells per group.
F Time course analysis of the splicing pattern of Chinese hamster Clk1 pre-mRNAs in control (CHO) and CHO (His9) cells by semi-quantitative RT-PCR. Arrows indicate the positions of PCR primers. The GAPDH mRNA was used as an internal control.
(D-F) RT-qPCR measurement of mRNA levels of Defa6 and Lyz2, two Paneth cell markers, and Ripk3, a TNF-induced cell-death gene, in ileum of the experiment in A.
A,B) Scatterplots showing that the wPRS correlates with A) adjusted baseline performance on the ECAS ALS-Specific, Total, Executive Function, and Language scores, and B) rate of decline on the ALS-Specific, ALS-Non-Specific, and Total scores.
(A) Beclin 1 (BCN1) interactors identified by yeast two‐hybrid technology. Proteins binding to BCN1 are listed and their interacting domains are indicated by black bars. Numbers refer to amino‐acid positions.
K, Reduced numbers of c-Fos-positive cells in CA3 of KO mice (n = 4 mice, WT; n = 5 mice, KO).
C Pathways and networks constructed using genes within 50 kb of AR binding locations enhanced in prostate tumors. Nodes and corresponding pathways are extracted according to interaction annotation. Literature‐based network is configured as PROSTATIC NEOPLASMS (Genomatix Mining).