EMBO/sd-character-level-ner huggingface dataset:
A GS∆44 myoblasts were transfected with an empty vector (CTRL) or with a CELF2a overexpressing construct (OE CELF2A) (Martone et al, 2016). Cells were collected after 10 days in differentiation medium (DM) and the RNA was analysed by RT-PCR for CELF2a expression and DMD exon 45 skipping. GAPDH was used as loading control. The arrow indicates the DMD exon 45 skipped band. Representative results are shown (n=3).
(c) Co-immunoprecipitation of endogenous p62 and Fap-1 in BJAB cells treated with 20 μM chloroquine for 16 h, followed by treatment with Fas ligand (50 ng ml−1) for 2 h at 4°C.
D. ChIP-qPCR shows increased EZH1 occupancy at promoters of non-fibrotic genes in AECs subjected to apical TGFβ1 for 72 h (mean + s.d., n = 3 biological replicates). Unspecific IgG was used as negative control. E. ChIP-qPCR shows no changes in H3K27me3 at promoters of non-fibrotic genes in AECs subjected to apical TGFβ1 for 72 h (mean + s.d., n = 3 biological replicates). Unspecific IgG was used as negative control.
The p53 domains and mutants used in this study are schematically represented in c
The ERMIT assay relies on the signaling properties of IRE1, one of the three ER stress sensors and reports for a dimerization event occurring in the lumen of the ER. The assay can be applied to heterodimerization or homodimerization events. B) Molecular modeling showing root-mean-square deviation (RMSD) plot for the MD simulation of the AGR2 WT and E60A mutant. The interaction-energies are defined as the sum of the short-range Coulomb interactions and the short-range Lennard-Jones potential between monomer A and B.
(E) The YAP-WW1/SMAD7-PY and STXBP4-WW/SMAD7-PY complexes show similar cumulative average trend and average binding free energy (∆G) within standard deviation (the shaded region) of one another.
(D). Allele-specific KAP1 association with Xist P2 in Fa2L cells following knock down of Luciferase (Control, black) and Rif1 (Rif1 KD, grey). cast indicates association with the castaneus Xist P2 promoter and 129 indicates association with the 129 Xist P2 promoter. Enrichments are presented relative to input DNA. Average ±standard deviation of two independent experiments.
(D) Deep pseudopupil imaging of PIP2 levels in the microvillar membrane of photoreceptors. The fluorescence of the PH-GFP probe is depicted. The protocol used is shown with red light illumination periods shown as red bars and flashes of blue light (a-f) used for image capture depicted. Representative deep pseudopupil images acquired at specified time points are depicted. Genotypes as indicated.
F Expression of DDX3 by immunohistochemistry in normal lung tissue.G DDX3 expression in squamous cell carcinoma.H DDX3 expression in adenocarcinoma.I DDX3 expression in small cell carcinoma.J Expression of DDX3 in different histological types of lung cancer. All data sets were compared against each other (chi-square test, P = 0.481).
B Substrates bound to exosites in the PS1 NTF at 4°C can be cleaved in the 37°C chase incubation in a L-685,458-dependent manner. Note that, although many of these substrates crosslinked only weakly at the exosites, their cleavage in the 37°C chase proved that these reflected functional substrate-binding states.C Substrates crosslinking in the exosites to NCT and PEN-2 cannot be cleaved.
A. Measurement of oxygen consumption rate (OCR), extracellular acidification rate (ECAR) and oxidative burst of monocytes from COVID-19 patients (COVID) and healthy controls (CTR). OCR was measured in real time, under basal condition and in response to mitochondria inhibitors: oligomycin (Oligo, 2 μM), cyanide-4-(trifluoromethoxy) phenylhydrazone (FCCP, 0.5 μM), and antimycin A plus rotenone (Rot/AA, 0.5 μM). Oxidative burst was measured in response to PMA/ionomycin (PMA/Iono, 1 μg/mL). Scatter plots show the quantification of basal respiration (indicated as Basal OCR), ATP-linked respiration (ATP-linked), maximal respiration (Max Resp), proton-leak, spare respiratory capacity (Spare), oxidative burst immediate response and basal ECAR. The maximal respiration kinetic range and the oxidative burst kinetic range are also reported and were obtained by analyzing the area under the curve (AUC) from the sixth to the tenth measurement and from the tenth to the thirteenth measurement, respectively. Data represent individual values, mean and standard error of the mean (CTR, n=12; COVID, n=13). Mann-Whitney test was used for statistical analysis. Exact p values are reported in the figure. Representative traces of OCR of monocytes from COVID-19 patients (COVID) and healthy controls (CTR) are also reported.
Heterologous expression of mouse TPCs tagged with TagRFP-T (in red) rescues the phagocytic defect of Tpcn1-/- and Tpcn2-/- BMDM, but a pore-dead TPC2-mutant (N257A) does not, n = 39-94. Images taken 40 min post- 3-μm bead addition.
Quantification of GBP1 recruitment to STm-GFP containing vacuoles (SCV) in MDMs pre-treated with IFNγ or left untreated (UT). Mean ± 95% CI of GBP1 fluorescence intensity measured on the indicated number (n) of SCVs for each condition from three independent experiments are shown.
C) Number of genes associated with the indicated processes, as revealed by functional analysis based on Gene Ontology and Reactome terms, (*): Apoptotic signaling pathway (p=0.0083), ER-associated degradation (p=0.0076), and lipid biosynthetic process (p=0.0059), respectively; (**): ER stress (p=0.0044), Protein folding (p=0.003), Calcium homeostasis (p=0.0022), N-glycosylation (p=0.0018), respectively.
In vitro membrane pelleting assay examining two Trs85 substitution mutants in the context of the TRAPPIII complex. In the absence of liposomes, all three complexes pellet slightly, however in the presence of membranes, only the wild-type Trs85-TRAPPIII complex is strongly enriched in the pelleted fraction. Representative of n=3 independent experiments. (S=supernatant, P=pellet)
B-K. Transmission electron microscopy (TEM) images of 5 week old adult retinas showing the overall structure of groups of ommatidia in (B) wild type; (C) ADAM17-/- mutant; (D) ADAM17-/Deficiency; (E, F) RNAi against ADAM17 and control (lacZ), expressed throughout the retina; (G, H) RNAi against ADAM17 and control (lacZ), expressed in the neurons; (I,J) RNAi against ADAM17 and control (lacZ), expressed in the pigmented glial cells; and (K) a kuz-/- mutant.
B Workflow for the comprehensive virus-host interactome analysis. Two different strategies, SFB-TAP and BioID2 proximity labeling, were applied in the study. Samples were analyzed by Q Exactive HF mass spectrometry (MS).
(F-I) 3D views of representative 232 x 232 μm2 fields of view of the AT (F, H) and endothelial layer (G, I) from infected LoCs reconstituted with macrophages at 1 (F, G) and 3 dpi (H, I). IL6 mRNA, and nuclear staining are indicated with the chartreuse and electric indigo LUTs, respectively.
BMDMs were costimulated with TNF (100 ng/ml) and SM LDH release in the cell culture supernatant were quantified at the indicated time points.
(C) Schematic illustration and representative photomicrograph of an organotypic culture of a nasal explant from E11.5 mouse embryos after 8 days in vitro. NE, nasal epithelium; NMC, nasal midline cartilage. Scale bar 500μm (150μm in inset).
(R) Quantifications of the proportions of %Dome (green bars), %negative (blue bar), %overlap (Dome and P1, yellow bars) and %P1 (red bars). For Dome positive area (domeMESO-Gal4, UAS-GFP/+, n=27, domeMESO-Gal4, UAS-GFP; THRNAi, n= 15 and domeMESO-Gal4, UAS-GFP; DdcRNAi, n= 18), negative and overlap areas (domeMESO-Gal4, UAS-GFP; THRNAi, n= 15, domeMESO-Gal4, UAS-GFP; DdcRNAi, n= 18) and P1 positive area (domeMESO-Gal4, UAS-GFP/+, n=27, domeMESO-Gal4, UAS-GFP; THRNAi, n= 15 and domeMESO-Gal4, UAS-GFP; DdcRNAi, n= 18). Data information: The quantifications in R represents mean with whiskers indicating maximum and minimum values, box indicates the lower and upper quartiles. The statistical analysis applied in R is Two-way Anova with Tukey's multiple comparisons test. 'n' represents the number of lymph gland lobes analyzed, *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001.
(F) Anti-Ki67 antibody was used to label proliferative myoblasts (red fluorescence) with DAPI labeled nucleuses (blue fluorescence) in paraspinal muscle. Scale bar, 25 μm. (G) Bar graph showing statistical analysis of positive rate of Ki67-labeled nuclei, n = 3 with more than 150 cells analyzed per n, **P < 0.01, by chi-square test (χ2 test). WT means wild types, Hetero means heterozygotes, and Homo means homozygotes.
C) A schematic overview of all available autoSP3 protocol versions. The autoSP3 procedure is provided with three options for reduction and alkylation and with post-digestion peptide recovery as described in the Appendix Protocols (A to D). Protocol A: one-step reduction and alkylation using a TCEP/CAA mixture for 5 minutes at 95°C, followed by autoSP3. Protocol B: two-step reduction and alkylation using DTT and CAA consecutively with 30 minutes incubation at 60°C and 23°C, respectively, followed by autoSP3. Protocol C: the core autoSP3 protocol omitting reduction and alkylation such that the user can flexibly pre-treat manually prepared samples. Protocol D: post-digestion acidification and recovery, delivering MS injection-ready peptides to a new sample plate.
Kaplan-Meier analysis showing cases from the Australian cohort (n = 73) delineated on the basis of expression of a set of hazardous genes, termed PC-1. Patients with the highest expression had a significantly poorer prognosis (red line, median survival: 11.6 months) compared with those patients with the lowest expression (blue line, median survival: 34.4 months, P = 0.01). The black line shows those with medium expression.
(G-J) Cbl is required for germline differentiation. Immunostaining of wild-type and CblEY11427/MB05683 germaria with anti-Hts to visualize spectrosomes and fusomes. White arrowheads indicate GSCs; the white arrow indicates increased number of spectrosomes.
Representative immunoprecipitation (IP) of HEK293 cells transfected with indicated cDNAs. (B) Deletion of the CT domain of human CTGF (CTGF-ΔCT_ΔTSP1 and CTGF-ΔCT) impairs the interaction between CTGF and LRP4ect-Flag. Predicted positions of full-length and shortened CTGF proteins are indicated by bars and/or asterisks.
(A) Serine phosphorylation of cPLA2α in response to GBS strain K79 in HBMEC pretreated with gefitinib or vehicle control and in EGFR knockout HBMEC.
C, D Quantification of immune cell and inflammatory markers (C) and pro-inflammatory cytokines (D) in adipose tissue of chow-fed (n = 5 in both genotypes) or HFD-fed (n = 11 in both genotypes) WT and NOD2−/− mice, *P = 0.04, **P = 0.02, ##P = 0.004, and #P = 0.04.
C RNA purified from wild type, abo1Δ and spt16-18 cells was analysed by northern blotting using a probe to the 3′ end of spbc19c7.11 (top panel). RNA (5 µg) used for northern blotting was analysed on an ethidium bromide stained 1% TAE agarose gel (bottom panel). Data are representative of two independent biological repeats.
Generation of suppressors of choline auxotrophy of cho2opi3, cho2opi3lro1, and cho2opi3lro1 pLRO1 on choline-free medium as indicated at 30 oC for 7 d.
(d-f) Three-dimensional architecture of the flagellar base, with the connecting piece in grey, the proximal centriole in green, distal centriole doublets in blue (A-tubule in light blue, B-tubule in dark blue) and singlets in pink, and electron-dense bars in yellow. The connecting piece was segmented semi-automatically with a neural network, while microtubules were traced manually.
A Histochemical stained roots from composite plants transformed with proMtNPF6.5:GUS (left column), proMtNPF6.7:GUS (middle column), proMtNPF6.6:GUS (right column).
(A) Blood glucose in 6‐ to 10‐month (mo)‐old mice (n=12-15), and (B) serum insulin levels in 10‐mo‐old fed control (Con) and KO mice (n=6).
(C) Cell viability (TO-PRO-3 FACS staining) of GT1-7 neuronal cells treated with 1, 3 or 10 µM of promethazine and co-transfected for 24 hours with either a control siRNA or a siRNA targeting C9orf72 mRNA and a construct expressing either 80 G4C2 repeats or 100 C4G2 repeats embedded in sense or antisense C9ORF72 fused to the GFP in the GA or PG frame.
(C) Quantification of mean (±SEM) EPSP amplitudes, in which 75 consecutive evoked events were averaged per cell, and then cell amplitudes were averaged per genotype. [UAS-RFP n = 8 cells, UAS-WR-dNmnat n = 7 cells, UAS-H30A-dNmnat n= 7 cells. 1-way ANOVA w/Tukey's multiple comparisons, DF=21, F=0.8596, p = 0.4383. UAS-RFP vs UAS-WR-dNmnat p = 0.8810 (NS), UAS-RFP vs UAS-H30A-dNmnat p = 0.9997 (NS)].
C Mitochondria were induced in YPL medium and mitophagy was assessed as described for Fig .
D. In contrast to controls (i), Tau AT180 antibody (magenta) that specifically recognizes the phosphorylated Threonine 231 of Tau protein distinctly localizes at the somas of SARS-CoV-2-positive neurons (AB4, green) (ii). At least four organoids from two different batches (n=2) are tested. Figures display scale bars.
(F) Expression of in vitro transcribed Aug-nLuc and CGG-nLuc reporters in rabbit reticulocyte lysate (RRL) in vitro translation system following pre-treatment with DMSO or SRPIN340. Error bars represent mean +/- SD (n=9 biological replicates). Data information: Statistical analysis was performed using Student's t test with Welch's correction. ∗p < 0.05; ∗∗p < 0.01
typical action potentials (APs) in controls (B, top panel) and typical NachBac-mediated APs showing lower threshold and long duration (B, bottom, the inset highlighting the long duration) in NachBac mice
(A) A schematic illustration of the siRNA assay in Caco-2 cells infected with SARS-CoV-2 to validate the antiviral efficacies of the consensus predicted metabolic targets. Caco-2 cells were transfected with siRNAs for 48 h prior to infection with SARS-CoV-2 (MOI=0.1). Four replicates were performed for each target. At 48 h post-infection, cells were subjected to staining with SARS-CoV-2 nucleoprotein (N) antibody and DAPI, and then imaged to determine the percentage of infected cells after each target knockdown (Methods).
A. Map showing the EBV epitranscriptome in CNE2EBV with induced EBV reactivation, or HK1 cells with acute EBV infection. CNE2EBV cells were treated with NaB (2 mM) for 24 h to reactivate EBV. For acute EBV infection, RNA of HK1 cells was harvested at 24 hpi. The m6A peaks, identified based on all MeRIP-seq data using MACS2, are indicated as pink bars. The input and MeRIP coverage are indicated with gray and orange bars, respectively.
F, F' Scanning electron microscopy (SEM) of P21 adult trachea shows reduced numbers of cilia of Ccno‐deficient MCCs. Remaining cilia are found in the central regions of the cell surface, and cell margins frequently lack the ciliary decoration (arrows).
Western blot against CB1 and GAPDH (used as loading control). Images belong to the same blot but to non-consecutive lanes as indicated by the boxes. Graph showing mean ± SEM CB1 protein levels normalized to GAPDH in extracts from cultured neurons from ASM-KO mice incubated or not with exogenous SMase (n = 5 independent cultures, Student's t-test).
J) Quantifications of Tie2-integrin colocalization for cells that have F-domain sheet (GFP+) attachment.
okp1-R164C suppressed the temperature-sensitive growth defect of cbf1∆ cse4-R37A. Serial dilutions of strains with the indicated genotypes were spotted on full medium and grown for three days at 30ºC or 37ºC. The original okp1-R164C isolate from the suppressor screen is indicated as "UV mutagenesis".
C. FISH with probes to GAPDH mRNA or oligo(dT) to detect poly(A)+ RNA in A549 cells without or with either NLS-RL-WT or NLS-RL-CM either mock transfected or transfected with poly(I:C) for 4 hours. Scale bar 5 micron.
Genes found to be down-regulated by PARPi as described above (p value < 0.05, 1.5-fold change) in either HT-sensitive cells (left) or CRPC cells (right) were queried against the expression of these genes in the Grasso et al data set in Oncomine. Benign = grey, primary PCa = blue, metastases = orange. Boxplot was generated using the mean expression of the PARPi down-regulated genes in the indicated data sets. Statistical significance determined by two-tailed Student"s t
E, F. Bclaf1 WT, KO-1 and -2 HeLa cells (E) or MEFs transfected with siCtrl or siBclaf1-1 and -2 (F) were pretreated with CHX (1 μg/ml) for 30 min and then stimulated with TNF (10 ng/ml) in the presence of CHX for 12 hours followed by western blotting analysis.
I: Schematic representation of ELDR-ILF3 mediated regulation of Cyclin E1 signaling. The arrow indicates activation.
(A) A549 cells of the indicated genotypes were either left untransduced or transduced with a lentiviral vector expressing PIDD1-V5 in its wild type form. Cells were treated either with DMSO or with ZM447439 for 24h and subjected to immunoblotting. N = 2 independent experiments.
(A) Average allelic ratio of single cells projected onto the UMAP plot. n = 220 X-linked genes per single cell. X-inactivation (average ratio <0.135) in red and X-reactivation (average ratio from 0.135 > 0.8) in green. Labels indicate the 5 different previously identified clusters. Dashed lines indicate the position of cluster borders (clusters obtained from Fig. 4D-F).
e, SPR-4 protects against Aβ neurotoxicity. Shown are Aβ worms (expressing a stably integrated Aβ1-42 transgene) and Aβ spr4(by105) worms. Neuronal degeneration does not occur in wild-type worms or spr4(by105) mutants in the absence of the Aβ transgene. Values represent the percentage of worms that retain five glutamatergic tail neurons at the indicated age (days), and are the mean ± s.d., n = 3. *P  0.05 by unpaired t-test.
F Quantification of FLUCSM::GFP foci disaggregation. % disaggregation is calculated as 100 - ratio of FLUCSM::GFP foci area relative to total muscle area at the +HS 24h time point to the +HS 2h time point. Data are displayed as mean ± SEM (in %) (N = 3). Statistical analysis was done using one-way ANOVA with Dunnett's multiple comparison test. n.s. = not significant, ** p ≤ 0.01. All strains harbor the sid-1(pk3321) allele.
G Protein levels were measured by immunoblotting using lysates of mouse liver tissues.
E HeLa cells were transfected with Mito-BFP and ActA-SEPT7-mCherry, fixed and labelled with antibody to Drp1 for widefield immunofluorescence microscopy. The scale bar represents 5 μm. Inset images highlight Drp1 and SEPT7 associated with sites of mitochondrial fission. Pearson's correlation coefficient from 3 independent experiments (mean ± SEM) shows that mitochondria in ActA-SEPT7 transfected cells recruit significantly more Drp1 than control cells (Mito-BFP transfected alone). Student's t-test, * = p<0.05.
(F) A PP2A-B56γ-BubR1516-715 complex was reconstituted (blue box) and peak fractions pooled and incubated with hSgo11-155. Following incubation this complex was analyzed by size-exclusion chromatography and fractions analyzed by SDS-PAGE (black box).
Fat (H,I) or lean (J,K) mass in the mice in (F) measured after the 4 weeks of treatment (H,J) or weekly (I,K); n=9-10.
(A) Normal APP and BACE1 endocytic trafficking diverge at early endosomes restricting Aβ generation. 1a. BACE1 endocytosis. 1b. APP endocytosis. 2. BACE1 recycling to the plasma membrane. 3. APP sorting to intraluminal vesicles. 4. APP delivery to the lysosome for degradation. 5. BACE1 cleavage of APP. 6. γ-secretase cleavage of APP-CTF (not represented). 7. Aβ generation.(B) In Bin1-depleted neurons, BACE1 accumulates in early endosomes raising Aβ generation in axons due to inhibition of local BACE1 recycling. Inhibition of recycling likely results from inefficient scission and exit of tubular BACE1 carriers from axonal early endosomes to which Bin1 preferentially associates.(C) In CD2AP-depleted neurons, APP accumulates in early endosomes raising Aβ generation in dendrites due to inhibition of local APP degradation. Inhibition of degradation likely results from impaired sorting of APP in dendritic early endosomes to which CD2AP preferentially associates. Inhibition of APP sorting away from the endosomal limiting membrane favours local APP processing.
A Structure of phosphoUb in space group P1 with 8 molecules in the asymmetric unit (Table ). Ub molecules are colored differently, and atoms for pSer65 are shown as spheres with red oxygen and purple phosphorous atoms.
A AGO4 and AGO6 were visualized by immunofluorescence microscopy using their specific antibodies. Yellow signals would be expected in the merged images if the two proteins co‐localize, as a result of the overlap of red and green channels. DNA (blue) was stained with DAPI.
A-H In situ hybridization experiments with an antisense probe for c‐Fos on coronal sections through the GG of wild‐type (WT; left panel) or GC‐G‐KO (right panel) mouse pups (P0-P4) exposed to warm (35°C; A-D) or cool (22°C; E-H) ambient temperature for 2 h. Panels (C, D, G, H) show higher magnifications of the boxed areas in (A, B, E, F). At 35°C (A-D), no c‐Fos expression was detectable in the GG of both WT (A, C) and GC‐G‐KO (B, D) individuals. Upon exposure to 22°C, strong c‐Fos expression was observed in the GG of WT pups (E, G), whereas c‐Fos expression was barely detectable in the GG of GC‐G‐KO animals (F, H). The data shown are representative of 10 independent experiments. Pups originated from six different litters for each genotype. Scale bars: 200 μm in (A, B, E, F); 50 μm in (C, D, G, H).I Quantification of c‐Fos‐positive GG cells in WT and GC‐G‐KO pups on exposure to 22°C for 2 h. All stained cells on every section along the rostrocaudal extent of the GG were counted; the results shown are based on the above‐mentioned 10 experiments. The number of c‐Fos‐positive cells in the GG of a GC‐G‐KO mouse was determined relative to that in a concomitantly processed WT pup; the latter number was set to 100%. Data are mean ± SD (n = 11 in each genotype), **P 0.0001.
Selection of the most suitable quality marker proteins for platelet contamination (blue dots) and (E) erythrocyte contamination (red dots) based on their abundance, the platelet/erythrocyte to plasma ratio and the coefficient of variation. Proteins that were only detected in platelets or erythrocytes, but not in plasma are aligned on the right side of the graph.
C, D Genomic views of relevant TF binding to Cebpa and Gata3 loci (supporting direct regulatory interactions identified in Figs 3A,B,C). The red arrow indicates a putative enhancer element, which is bound by Ebf1 and flanked by AcK27-rich regions.
(E) Different gRNAs were paired with dCas9-AsiA and dCas9-ω to profile the optimal gRNA binding distance. The dCas9-AsiA was verified in the wild-type strain (BW25113), and dCas9-ω was examined in the ∆rpoZ strain background.
a) Bar charts showing the relative surface of clones attached and not attached between 3 and 24 weeks after induction at P21 or P42. Data are represented as mean ± s.e.m.
A-D Panc02 cells with stable expression of luciferase were implanted subcutaneously into C57Bl6/N mice. Six days later, tumors were injected three times per week with 108 ifu of adenovirus encoding shRNA. (A-C): Data plotted as mean ± SEM; n = 4 animals in control (shNC) group and n = 3 animals in knockdown (shTBL1) group; significantly different (P < 0.05) between control (shNC) and knockdown (shTBL1) *. (A) Tumor volume determined by transcutaneous measurement with digital calipers; P-values: 9.21 × 10−3 at day 15, 6.02 × 10−4 at day 18, 2.49 × 10−4 at day 20; two-way ANOVA with Bonferroni post-test. (B) Luminescence of tumors after intraperitoneal injection of firefly d-luciferin; P = 0.0133 at day 20; two-way ANOVA with Bonferroni post-test. (C) Tumor mass at necropsy; P = 0.0299, one-sided Welch's t-test. (D) Luminescence images of one representative mouse in each group.
D. Confocal images of mitochondrial morphology in Drp1-/- 293T cells treated with scrambled siRNA and Dyn2 siRNA as indicated, followed by transfection with empty vector (left panel) and Myc-hFis1 (right three panels). Cells were stained with MitoTracker (red) followed by immunostaining with anti-Myc antibody (green). Representative examples of tubular, fragmented and tubular cluster phenotypes are indicated.