EMBO/sd-character-level-ner huggingface dataset:
B. Control cells or cells collected 8h post-transfection with pIC. Then, the levels of CXCL10 mRNA and the indicated CSRs were quantified by qRT-PCR. GAPDH mRNA was also measured and used as a reference. Fold increase of each CSR in treated versus control cells is shown. Fold changes higher than 2 are indicated at the top of each bar. The experiment was performed at least twice in triplicate and each value shows the average (n=6). Error bars indicate standard deviations and asterisks mark significant differences (ns, non-significant; * denotes p<0.05, ** p<0.01) obtained with a two-tailed non-parametric Mann-Whitney U-test.
D) Graphical representation of the scored TA weight (n=6). The dashed area indicates the range of native TA mass depending primarily on mouse weight and age, statistical significance was analyzed by Anova test (P < 0.05 was considered significant: *=0,0306).
J A proposed working model to illustrate how the USP19-Beclin-1 axis positively regulates autophagy and negatively regulates type I IFN signaling.
Examples of the three genotypes found at Mendelian frequencies (see Appendix Table S1) on 2.5 dpc embryos.
(b) Reduced levels of soluble mTOR in brain lysates from mice expressing mutant huntingtin (M1, M2; n = 9) compared with age-matched wild-type littermates (C1, C2; n = 9; P 0.001, unpaired t-test).
IP/Input ratios for the indicated factors, for ten Jpx#9 sequences with shuffled sequences in bases 80-109, WT sequence of Jpx#9 or 3 repeats of the SIRLOIN element ('3X SIRLOIN'). Boxplots are as in Figure 1C.
human neurons differentiated in culture for 30 days from ReNcell VM neuronal progenitor cells (B) were serum-starved in Hank's balanced salt solution for 2 hours. Next, the cells were imaged immediately (starved), after which either amino acids (R+L) or insulin were added. Thirty minutes later the cells were imaged again. Finally, the mTOR inhibitor, Torin1 was added, and after an additional 30 minutes, the cells were imaged for the last time. Histograms represent changes in the fraction of enzyme-bound NAD(P) H (a2%) for each condition. Note that insulin and amino acids significantly increased the a2% values, which was reversed by Torin1-mediated inhibition of mTORC1. Average data from 5 fields of view per condition are shown. Statistical analyses were performed using Student's two-tailed unpaired t-test
(A-D) Results of high-resolution quantitative mass spectrometry analysis identifying proteins with increased abundance in stimulated synaptoneurosomes. Volcano plots (Whitney-Mann test, Benjamini Hochberg correction, n=5 per group) showing abundance of identified proteins in NMDAR-stimulated (20 min) synaptoneurosomes as compared to unstimulated using iTRAQ8-plex (A) and TMT10-plex (B) labelling methods. Mitochondrial proteins are depicted in orange. The vertical line defines the p-value statistical significance cut-off. For nine mitochondrial proteins their mRNA abundance on polyribosomes was quantified, the data is presented on Figure EV2. (C) Biological functions of proteins identified as significantly upregulated after NMDAR stimulation (assembled from all three proteomic analyzes: LFQ, iTRAQ8, TMT10
E. Average amplitude of mEPSCs (pA) for only naspm treated neurons under each of the conditions, TTX, TTX + DHPG, and TTX + DHPG + 2APB/dantrolene. F. Average frequency of mEPSC (Hz) for only naspm treated neurons under each of the conditions, TTX, TTX + DHPG, and TTX + DHPG + 2APB/dantrolene.
PCA of the different subpopulations from IgG or αDll4 treated embryos based on normalized gene counts. PCA considering the DEG according to the treatment specific for each subpopulation.
Relative mRNA expression (ASK1F/F n=13 mice; ASK1+hep n=14 mice) of respective genes involved in inflammation and fibrosis in liver of CCl4-injected mice. Values are expressed as mean ± SEM.
Flow cytometry analysis of EMPs (Ter119- Kit+ CD41+ CD16/32+) and early erythroid progenitors (Early E: Ter119- Kit+ CD41- CD71+ CD44+) in wild type and Sl/Sl E11.5 FL. EMP and early E data are the mean (±SD) of 6 wild type and 4 Sl/Sl biological replicates, with a total of 10 wild type and 6 Sl/Sl embryos analyzed in pools of 1-3 FL per genotype. Bar graphs on the right show corresponding absolute cell numbers (nr) per FL. Total FL cell counts are the mean (±SD) of 12 wild type and 13 Sl/Sl embryos. Tail somite range: 10-16 (wild type), 12-15 (Sl/Sl). Note that although EMP frequency in Sl/Sl FL is increased, their absolute number is severely decreased.
(B) Flag immunoprecipitation assay. Flag-tagged Cyclin B2-WT, Cyclin B2-4A, or Cyclin B1 were expressed in 293T cells and purified with anti-Flag M2 beads. Subsequently, the beads were incubated with mitotic HeLa lysates for 2 h, and, following extensive washes, immunoprecipitatates were resolved by SDS-PAGE and analyzed by Western blotting using anti-Flag antibody and anti-Mad2 antibody.
NK cell-mediated killing of RELA ArCK cells was compared to clones harboring an empty vector. ArCK RELA knock out cells were generated and the NK cell-mediated cytotoxicity was measured as described in the method section. Dot plot of individual data points and mean were presented. n=2 biological replicates; ArCK-c1 vs ArCK RELA-c1, p= 0.70, n.s.; KS test. The effect of inactivating RELB on NK cell-mediated cytotoxicity in ArCK cells. The same experimental methods were used as described in (A). n=3 biological replicates; ArCK-c1 vs ArCK RELB-c1, p= 0.47, n.s.; KS test.
(D) quantification of the relative number of X1 cells [n=3 biological replicates; data were normally distributed (P>0.05 as per Shapiro-Wilk test) and analyzed by multiple t-tests with Holm-Sidak correction for multiple comparisons].
E, F COS‐1 cells were treated with ATP8A1 siRNA1 for 72 h. Cells were pulsed with Alexa 594‐CTxB for 5 min and chased for 15 or 60 min. Cells were then fixed and stained for GM130. In (E), representative images are shown. In (F), the Pearson's coefficient between CTxB and GM130 after 60‐min chase is shown. Data represent mean ± SD (n > 26 cells from three independent experiments). ***P 0.001; two‐tailed Student's t‐test. Scale bars, 10 μm.
IB analyses of HEK293 cells transfected with β-catenin siRNA or control siRNA for 48 h and then treated with L-cell-conditioned medium (L-CM) or Wnt3a-CM for 8 hr
(B) HEK293A cells labelled with [14C]valine, as described in Material and Methods section, were pretreated with 10 μM anisomycin for 30 min before incubation in either full medium, EBSS, or EBSS with leupeptin for 2 h. Cells were then analysed for long‐lived protein degradation (data are represented as mean±s.e.m. of triplicates, representative of two experiments, EBSS untreated versus anisomycin treated (P=0.0363); EBSS untreated versus leupeptin treated (P=0.0001), Student's t‐test).
A, B, C The layer thickness and neuronal number within each layer was assessed using layer-specific markers in Kcc2-/-and Kcc2+/+ embryos at E18.5. Cux1 was used to label layers II-IV (A), Ctip2 to label layer V (B), and Tbr1 to label layer VI (C). Dashed white lines in the representative images in (A-C) indicate upper and lower layer boundaries. Sp, subplate. Statistical significance was determined using Kruskal-Wallis test with Dunn's post hoc (neuronal numbers) and one-way ANOVA with Holm-Sidak's post hoc (layer thickness). Data are presented as mean ± S.E.M., n = 11 embryos for both genotypes. Scale bar = 50 µm.
(A) Schematic for the generation of differentiated colonic epithelial cells grown in a monolayer.
(A) Representative time-lapse images showing tumors without CAR T cells (upper panels) or with CAR T Cells (lower panels). Tumor cells with low and high intracellular calcium appear in blue and red, respectively. CAR T cells appear in light green. Red arrows indicate tumor cells with elevated calcium. Scale bar, 5 µm.
A Transcriptional profiling of MdCXIP1 in Md/Mx and Md/Mb under Fe deficient and Fe replete conditions.
H, Histogram depicting the percent of proliferating (Ki67+) cells transfected for 24 h with plasmids expressing control (GFP) or Trnp1-IRES-GFP and its different mutant/truncated forms-IRES-GFP in dissociated E14 cortical cells. Biological replicates: GFP=21; Trnp1=15; FLAGTrnp1=10; mutCC=5; ∆1-16=7; ∆1-1-56, ∆1-97, ∆1-140=3, ∆95-223=5 and ∆140-223=4.
A The schematics of the WT and the mutant (∆5′/∆3′) with deletion of the 5′ and 3′ terminal regions are shown as Figure 1A. The positions of the NEAT1 probes used in SRM (blue) and EM (orange) are shown.
J. Proposed model. Left panel: active (yellow star) membrane-bound Rab7 can partner with its effector RILP to mediate dynein-dependent minus-end-directed transport of late endosomes and/or lysosomes into the perinuclear region, toward the microtubule organizing center (MTOC). Left middle panel: a subpopulation of Rab7-positive vesicles acquires Arl8b, forming a hybrid identity compartment. Arl8b in turn recruits the effector SKIP through the N-terminal RUN domain (red), as well as VPS41 and the core HOPS subunits to endosomes. Right middle panel: SKIP is now in the position to engage Rab7 using its C-terminal segment featuring the KMI motif. This promotes acquisition of VPS39 and reconstitution of the HOPS complex, providing a platform for recruitment of the Rab7 GAP TBC1D15 (yellow) not associated with mitochondrial membranes. Right panel: the resulting Arl8b/SKIP/HOPS/TBC1D15 complex induces inactivation (grey star) and removal of Rab7 from the membrane, while maintaining Arl8b/SKIP identity and liberating the endosome for kinesin-dependent transport toward the microtubule plus-end, into the cell periphery. Regulated disengagement of Rab7 thus enables orderly selection of transport route.
(C) In inactive conditions, Gal4 still binds DNA, but is fully repressed by Gal80.
(I) GalNAc-T2 may affect tight junction formation and integrity. Upper panel, TEM of WT and GALNT2 KO organotypic tissue sections, where tight junctions are marked with asterisks. Lower panel, IF staining of WT and GALNT2 KO for tight junction marker occludin (scale bar - 50 μm). Inserts depict 3x zoomed in partial images (scale bar - 50 μm).
(C,D) Local structures of top and front views of Paired RAG STC near the 12RSS integration site. (E,F) Local structures of top and front views of Dynamic RAG STC near the 12RSS integration site.
A) Cells expressing the indicated GFP-fusions (green) were loaded with Alexa647-Transferrin (red; arrowheads indicate transfected cells) for 15 minutes, fixed and the morphology of the transferrin positive recycling endosomes analysed by confocal microscopy. Scale bars = 10 μm. Arrows in inset indicate the juxtanuclear ERC
Splenocytes from P. chabaudi chabaudi infected mice were stained with fluorescent antibodies and analyzed by flow cytometry. (I) Representative contour plots showing CTLA-4-expressing cells among TREG and CD44+ CD4+ T cells.
Human H1299 cells were treated with control (CTR) or indicated siRNAs two days before drugs were added to the media for dose-dependent viability assays. Cell extracts prepared at the time of drug addition were immunoblotted as indicated. SMC1 was used as a loading control.
A. Overview of central cleft shows path of target RNA. Seed, bridge, and supplemental regions indicated.
(I) S-phase length of E13.5 control and DKO APs and BPs, calculated from the data of panel (H, yellow) as described in Appendix Methods. Data are means ± SEM (n=4 embryos, 3 litters).
Under no stress (light green shading), BiP binds to the lumenal domain of disulfide bonded monomer and dimer ATF6α, preventing ER exit (Step 1). In step 2, under conditions of ER stress (light red shading), ERp18 or other PDI family members could reduce ATF6α disulfides resulting in the release of BiP from ATF6α. ERp18 binds, possibly before or after BiP release, and regulates ER exit. Reduced ATF6α is subsequently packaged into COPII vesicles and transported to the Golgi apparatus (step 3). The regulated binding and release of chaperones and oxidoreductases ensures that only reduced ATF6α, which is the optimal substrate for S1P, is transported to the Golgi. Sequential cleavage by S1P and then S2P, leads to membrane release and production of ATF6-N respectively (step 4). ATF6-N, traffics to the nucleus to transactivate genes required to restore ER homeostasis. The fate of the lumenal domain is unknown but maybe secreted. In the absence of ERp18, ATF6α rapidly exits the ER and is cleaved by an unknown post-ER localised protease to produce a fragment that is inefficiently processed by either S1P or S2P.
C. Primer extension reactions were performed on total RNA from cells transfected with siRNAs as described in B. Stops corresponding to position C34 in mt-tRNAMet were quantified in three independent experiments and results are shown graphically as mean ± SD.
B Immunoblotting of protein extracts from PaSCs and CAFs, using anti-sst1, anti-α-SMA, anti-P-S6 or anti-GAPDH (loading control) antibody (representative of n = 3).
B. A sequence comparison of VP-peptide motifs that interact with the COP1 WD40 domain. The VP core is colored in red and the anchor residues in orange. The peptide sequences are numbered on a register where the V in the VP is 0.
CHD1 depletion leads to decreased (C) CtIP and (D) RPA1 recruitment to I-SceI-induced DSB in U2OS19 ptight13 GFP-LacR cells. CHD1 was depleted in U2OS19 ptight13 GFP-LacR cells by siRNA and 48 h after transfection cells were treated with doxy for 16 h and co-immunostained for γH2AX and CtIP or RPA1. The number of cells with CtIP or RPA1 foci from (C) and (D) were counted and represented the mean in the graph as percentage of foci positive cells as ± SD (n=3), more than 50 cells were counted. Scale bar 5 µm.
(B) 3D structural modelling of glycosylated trimeric Spike (green with glycans in yellow) interacting with glycosylated human ACE2 (purple with glycans in salmon). The CRD of hCLEC4G (cyan with Ca2+ in orange) was modelled onto Spike monomer 3 glycan site N343 (complex type glycan with terminal GlcNAc in purple-blue) and the CRD of hCD209 (dark blue with Ca2+ in orange) was modelled onto the Spike monomer 3 glycan site N234 (Oligomannose structure Man9 in red). Structural superposition of CLEC4G and ACE2 highlights sterical incompatibility.
I The mRNA level of CD39, ENTPD2 and ENTPD3 in the hippocampus of susceptible mice after CSDS (n = 7, 8 mice. CSDS vs control, CD39 P = 0.0002, ENTPD2 P = 0.0025, Student's t test).
ACE2 mRNA expression in organoids grown in FM or in basic medium and either untreated or treated with IFN-γ (n=3). Data are presented as mean +/- SD ,*: p≤0.05, **: p≤0.001, ***: p≤0.0001, as determined by one-way ANOVA, followed by Tukey's multiple comparisons test
Based on promoter activity, we allocated target gene promoters along three archetypical expression patterns illustrated by a schematic triangle.
A) MALDI imaging of key metabolites in IDHwt (P3) and IDHm (E478) glioma PDX, compared to control brain (CB) sections.
G No change in DHHC2 expression in zygotes of the dhhc2::6HA parasite-derived mutants with individual gene disruption of cdpk4, hap2, and dozi.
D. Schematic illustration of consensus c-Myc binding sites in lncRNA-MIF gene promoter. The indicated pGL3-based luciferase reporter constructs were generated to examine transcriptional activities of three putative c-Myc binding sites MIF1, MIF2 and MIF3 in response to c-Myc induction. MIF1-M, MIF2-M and MIF3-M indicate their corresponding mutant binding sites which are shown in the open boxes.
mRNA in situ hybridization images showing expression of Cwh43 mRNA in the mouse brain. Enclosed areas containing potions of the ventricle, hippocampus and dorsal thalamus are shown at higher magnification on the right. Arrowheads point to choroid plexus. Scale bar is approximately 400 µm.
L, M H&E staining and quantitative analysis of MSCs-mediated ectopic bone formation. Scale bar, 50 μm. Results are shown as mean ± SEM; n=8; *: p<0.05 and **: p<0.01 by ANOVA with Tukey's post hoc test
(D-E) Subcellular localization of Ams1 (D) and Ape4 (E). Wild-type (WT), nbr1Δ, sst4Δ, and atg1Δ cells were grown to mid-log phase in EMM medium and examined by live cell imaging. In (D), Ams1 was endogenously tagged at its C-terminus with mCherry. In (E), Ape4 was endogenously tagged at its C-terminus with GFP and in the same cells GFP-binding-protein (GBP) fused 3xUb was expressed under the P41nmt1 promoter. Cpy1 is a vacuole lumen marker. Scale bar, 3 μm.
A Plasmids containing human CD45 (hCD45) genomic DNA from intron 3 through intron 7 with a wildtype (I3-I7) or mutated exon 5 CTCF binding site (I3-I7*CTCF) were methylated with M.SssI and confirmed through BsaHI digest. Methylated and unmethylated minigenes were transfected into CHO cells for stable clone generation.
Left panel: Representative blots showing protein levels of YAP and phosphorylated YAP (Ser127) in control (si-Ctrl) and YAP knockdown (si-YAP) hOSEs. Protein levels were detected by Western blotting. β-Actin was used as a protein loading control. Right panel: Cell proliferation (cell number) in control (si-Ctrl) and YAP knockdown (si-YAP) hOSE cells.
Cellular H2O2 (HyPer) was evaluated in two melanoma cell lines upon TMX1 kd and TMX3 kd. (F) Exemplary ratiometric images (F505 nm / F420 nm) are shown for WM3734 and Mel Juso. Quantification of basal cellular H2O2 in WM3734 (G) and Mel Juso (H) cells. In (G-H), data are presented as mean ± SEM (n values: WM3734: control=168, TMX1 kd=209, TMX3 kd=192; Mel Juso: control=297, TMX1 kd=343, TMX3 kd=440). In (F) scale bars: 10 µm; color code: WM3734: color code: blue=0, red=3; Mel Juso: color code: blue=0, red=1.5.
(C) HeLa cells stably expressing GFP‐GATE‐16 were transfected with non‐targeting siRNA or a pool of LC3 siRNAs and treated as in (A). The cells were subjected to immunostaining with anti‐p62 after fixation, and analysed by confocal microscopy. The GFP intensity of three independent experiments was measured as described in 'Materials and methods' (right panel). Scale bar: 20 μm.
J. Quantification of in vitro TUNEL signal of PeTa cells after 6 days of 100 nM GSK-LSD1 or vehicle treatment. Representative images in Appendix Fig S1B. n = 8, ***p = 0.001 (Vehicle vs GSK-LSD1; unpaired Student's t-test). ROI, region of interest.
D, Average profiles of BRPF3 and H3K14ac ChIP-seq signal on ± 2.5kb around the centre of (top) BRPF3 and (bottom) ORC1 genome binding sites.
(E) GalNAc-T2 is important for cell to matrix adhesion. HaCaT WT and GALNT2 KO cells were used in a cell to matrix adhesion assay using plates coated with different ECM components. Data is presented as average + SD of 3 independent experiments and is normalized to WT. ANOVA followed by Dunnet's multiple comparison test was used to compare mean relative adhesion of 2 different clones of GALNT2 KOs to WT. * p ≤ 0.05; ** p ≤ 0.01.
(B) Induction of TnpR from Pcumate results in a loss of cell viability on tetracycline plates. Each spot is a 10-fold dilution.
c, Intracellular glucose concentrations in untreated and ADR-treated control;Bcl2 (that is, senescent) versus Suv39h1-;Bcl2 (that is, non-senescent) lymphomas in vitro (as in d-g). Results represent means ± s.d. (n = 5 each).
F Transcript levels of Sln in skeletal muscle (tibialis anterior) of 8-10 week old WT and KO mice housed at RT. (n=4-5 each gender). G Transcript levels of Sln in skeletal muscle (tibialis anterior ) of 8-10 week old male WT and KO animals housed at RT. (n=5).Data information: Transcript levels were normalized to 18S. All values shown are mean ±SD. * = p < 0.05; ** = p < 0.01. (two-way ANOVA with multiple comparisons F, ; unpaired student's t-test in G.
C Quantified decrease in SOX9 protein levels following inhibition of YAP using verteporfin (VP) in activated mouse HSCs expressed relative to DMSO control (n=3).
(B) Relative mRNA levels of FX, Vtn and TSP1 in liver B220+CD11c+NK1.1+cells stimulated with LiCM or LuCM. Shown are averages (N = 6/group) with SEM and one-way ANOVA
p16-3MR mice were treated with vehicle (PBS, 7 consecutive days), doxorubicin (5 mg/kg, 3 consecutive days) or abemaciclib (50 mg/kg, 7 consecutive days). 15 dpt, plasma was collected and expression levels of CXCL1 measured by ELISA (H) Data information: Data are means ±SD. One-way ANOVA *p<0.05, **p<0.01, ***p<0.001, N.S.= Not significant.
LYVE1 immunofluorescence (red) counterstained with DAPI (blue) (D) in back skin sections from mice treated intradermally with Control or Clodronate liposomes. n= 3 - 4 skin samples per mouse, n= 3 - 4 mice. Scale bar, 100 μm. epi, epidermis; der, dermis.
[D] flg22-induced MPK3/MPK6 phosphorylation in Arabidopsis is not decreased by DA. Kinase assays were performed at 5 min after flg22 treatment. Three independent experiments were performed and similar results were observed.
A) Immunoblot analyses showing MAPK phosphorylation after flg22 induction in Col-0 and in mkkk7. Protein extracts were made from seedlings treated with 1 μM flg22 and samples were taken at t=0, 10 and 30 min post induction. The p44/42 antibody was used to detect phosphorylated MAPKs. Position of the individual phosphorylated MAPKs is indicated at the right. Equal loading of proteins is shown with an α-Actin antibody as a loading control (bottom panel). Three biological replicates were done with identical results
C. Normalized blood cell counts in Ssrp1fl/fl; CreERT2+/+ mice treated with vehicle or tamoxifen on day 7 after start of treatment. Mean ± SD, * indicates p < 0.05 (unpaired t-test). n = 3 mice.
(I-L) As in A-H, except that iBMDM from IKKβ-CXCR3-Cre (flox/flox) (IKKβ (fl/fl) or WT mice were co-stimulated for 1 h with 100 ng/ml LPS and 10 μM nigericin or left unstimulated. Similar results were obtained in two independent experiments. Data information: In all panels, scale bar = 50 μm.
Experiments were performed using human primary monocyte-derived macrophages. (G) Intra-phagosomal proteolysis in human macrophages was monitored following uptake of DQ Green BSA / AF594 latex beads. TPL-2 catalytic kinase activity was blocked by pre-treatment with 10 μM C34 for 1 h (n = 4 wells). (H) Intra-phagosomal acidification in human macrophages was monitored following uptake of BCECF-coupled latex beads (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 ****.
Concentration-dependent binding of rCC1-HIS to wild type (WT), ∆bac and ∆bac + pLZ.bac complemented A909 strains. Mean and SD values are reported for n = 3 independent flow cytometry experiments.
C. Scheme of the Elongator and rElp456 mixing experiment. Recombinant Elp456 subcomplex (rElp456) was purified from E. coli and mixed with native yeast Elongator in regular salt conditions. The mixture, as well as rElp456 alone, were then subjected to glycerol gradient ultracentrifugation.
(a) Rates of degradation of long-lived proteins in control mouse fibroblasts or RARα(−) or LAMP-2A(−) (L-2A(−)) cells left untreated (None) or treated with 20 μM of the indicated compounds. Values are expressed as the fold change in proteolytic rate relative to the rate in untreated cells for each group; n = 3.
Immunoblots represents the knockdown efficiency for IRE1α and PERK protein in J774.2 cell line transduced with lentiviral particles carrying gRNA against the IRE1α or PERK gene.
F. Deconvolved inverted fluorescence micrographs of Heh1-VN Snf7-VC BiFC signal in a chm7Δ strain with either an empty plasmid ("-"; pRS416) or one expressing CHM7 (pRS416-HA-CHM7). Cell borders outlined. Scale bar is 5 μm.G. Plot of the percentage of cells with BiFC signal from F. Error bars are SD from the mean of each replicate. p values from un-paired student's T-test where ns is p > 0.05. ***, p ≤ 0.001.
mRNA levels of TMX1 (A) and NFAT1 (B) in primary melanocytes, keratinocytes and melanoma cell lines. data are are normalized to the expression of TBP and are presented as mean ± SEM (n≥3).