EMBO/sd-character-level-ner huggingface dataset:
B. Representative RFP immunostaining from the liver of Tie2-GFP mice (left panels) or Tie2-IFNα mice (right panels) at the indicated time points after 5x105 CT26-RFP intrasplenic injection. Arrowheads highlight single or clustered RFP positive cells; scale bars=100μm.C. Immunostaining quantification of hepatic CT26-RFP arrival (5 minutes post-injection: Tie2-GFP n=6, Tie2-IFNα n=2) and expansion (day 3 post-injection: Tie2-GFP n=6, Tie2-IFNα n=3; day 7 post-injection: Tie2-GFP n=5, Tie2-IFNα n=3) in the liver of Tie2-GFP mice or Tie2-IFNα mice that were injected with 5x105 CT26-RFP as described in B. Data pooled from two independent experiments; mean values are shown; error bars=S.E.M.; p-values were calculated by Mann-Whitney test. The increased percent of RFP+ areas in the liver of Tie2-GFP mice was statistically significant (p=0.0009 by one-way Anova test, not reported on graph).
C-G) Representative images showing that Hh staining normally localised to a ring like structure (yellow arrows), becomes delocalises to the glial cytoplasm upon htlACT overexpression, quantified in (E) (n=4, 6 brain lobes). Glial cells are marked with repo-GAL4>GFP. (E-F') are zoomed in images of (C-D').
Immunoblot analysis of WT, NLRP3 KO (F) THP-1 cells infected with ZIKV (MOI=1) for the indicated time points.
quantification of germband macrophages in control embryos and those expressing different RNAis against mitochondrial OxPhos Complex III (or an RNAi against Complex V. For (H) control (n=34 embryos) vs Complex III RNAi 1 (n=20) p=0.0001; vs. Complex III RNAi 2 (n=18) p=0.027; vs. Complex III RNAi 3 (n=16) p<0.0001; vs. Complex V RNAi (n=14) p<0.0001. Data information: show Stage 12 embryos. Complex III RNAis target Cyt-c1, UQCR-cp1-2, for Complex V, ATP synthase F1F0. Mean±SEM, **p<0.01, ***p<0.001, ****p<0.0001. one-way ANOVA with Tukey's (H).
F. ZNF853 localized to the nucleoli in U-2 OS cells (HPA067690). Data information: Protein of interest is shown in green, nuclear marker DAPI in blue and the reference marker of microtubules in red. Scale bar 10 µm.
Lipid overload in autophagy-insufficient state (Atg7+/−) leads to increased accumulation of lipid due to defective lipophagy. Autophagy insufficiency causes delayed turnover of mitochondria and mitochondrial dysfunction, which leads to augmented inflammasome activation when challenged with inflammasome activators such as lipid. Combined effects of increased lipid content, augmented inflammasome activation and their interaction lead to deteriorated insulin resistance and diabetes.
SPPL2c protein levels were analysed in germ cell populations from testis of wild type mice sorted for their DNA content which was determined by Hoechst 33342 staining as depicted in Fig EV4D. While for 4C, 2C and 1C fractions 10 µg of protein were loaded, for the testis control samples (=total lysates) 20 µg of protein were subjected to electrophoresis. *, non-specific band.
(C) Association between IKBKE (IKKε) and PSAT1 mRNA overexpression evaluated by a chi-squared independence test. The + sign indicates samples with significant (p<0.05) overexpression of IKBKE or PSAT1. Number and percentage of samples, as well as the Chi-square values are shown.
(F) IHC analysis of the islets from Leprdb/db and Lepob/ob mice at the indicated ages using anti-Pdia4 antibody and hematoxylin. Scale bar = 100 μm. The dash circles indicate islet regions. Data information: Data from 3 experiments are presented as the mean ± SD.
(G) Representative confocal images of β-catenin and UBTD1 in DU145 under resting (Ctrl), after calcium chelator treatment (EGTA) and recovery (Rec) conditions. Nuclei were stained with DAPI (Blue) on the MERGE image.
Western blot analysis showing depletion of ORP3 in the ORP3−/− hTERT-RPE1 cell clones. GAPDH served as a loading control.
6-week-old male CD36 knockout mice were administered with AAV-TBG-wildtype-CD36, wildtype-CD36 plus KLF10, palmitoylation site mutant CD36, mutant-CD36 plus KLF10 through tail vein injection, and then kept on WD/CCl4 for 12 weeks. n=5 per group. (E) Immunofluorescence staining of CD36 and β-catenin. (F) Quantitation of CD36 positive area. (G) Co-localization rate of CD36 and β-catenin. Data information: * P <0.05, ** P <0.01, *** P <0.001. Results are shown as mean ± SD. 1-way ANOVA
A,B RPE cells expressing shRNAs specific to lamin A/C or nesprin 2 (shNesprin 2, clones #1 and #2) were stained for G-actin with DNase I (green). Representative images are shown (A). Scale bars, 20 μm. The proportion of nuclear G-actin fluorescence intensity to the whole cell was measured (B, n ≥ 67).
single-cell quantification related to the data in a and b. (c) cytoplasmic [Ca2+] after ionomycin; (d) maximal cytoplasmic [Ca2+] after TG; (e) increase rate of cytoplasmic [Ca2+] when extracellular Ca2+ is applied; (f) decrease rate of cytoplasmic [Ca2+] when extracellular Ca2+ is removed in NKT1 and NKT2 cells which have similar Ca2+ plateau level (iso-cells; 900-1200nM for control group (a), and 400-700nM for CCCP group (b)).
(d) HeLa cells stably expressing GFP-VPS35 WT and D620N were depleted of endogenous VPS35 using 40 nM of siRNA, and subsequently immunostained for TGN46 and endogenous ATG9A and subjected to confocal microscopy. (e) Colocalization between TGN and ATG9A is expressed in terms of the Pearson's Coefficient. n=25 cells (WT) and 33 cells (D620N). Error bars represent s.e.m. and **P=0.01 by 2-tailed Student's t-test. Scale bars in (a-d), 10 μm.
G. Representative western blot showing changes of overall O-GlcNAcylation (upper panel), phosphorylation status of each target protein (middle panels) or pro-caspase-3 cleavage (lower panel) in THP-1 cells treated with Stx2a (10 ng/mL) for 9 h in the presence or absence of overexpression of Akt (wild-type or T305A/T312A). Data information: Error bars for bar graphs are presented as mean ± S.E.M. Statistical analysis was performed using two-tailed Student's t-test. *P < 0.05; **P < 0.01; and ***P < 0.001.
C The distribution of endogenous TFG was examined in cells stably expressing low levels of mRuby‐Sec23A (Sec23A) using SR‐SIM (n = 10). Scale bar, 5 μm. Inset scale bar, 1 μm.
A-B. Fluorescent images of 1 day old adult fly retinas, stained with BODIPY (green) and FM-dye (red) to mark lipid droplets and photoreceptor membranes respectively: (A) wild type; (B) ADAM17-/-, both reared in the dark. Scale bars: 10μm.
(i) Immunostaining of 5caC shows that TCF20 depletion increased 5caC level. White dashed lines show the cells infected with lentivirus. Scalebar 25 μm. (j) Statistical analysis of the 5caC fluorescence level. n=20 cells, and P<0.0001. Data information: Error bars represent the means ± S.E.M. Two tailed unpaired T-tests were used to analyze the data, n.s. (no significant difference), p<0.05(*), p<0.01(**). and p<0.001(***).
A. Linear representation of the structure of EML4-ALK V1 and V3 variants and the deletion 12N blade mutant including residue numbering indicating domain boundaries.
I-J. Quantification of capillary number per area (mm2; I) and average of capillary cross-sectional area (µm2; J) in mdx-Control and mdx-CriptoMy-LOF diaphragm muscles. Data are mean±SEM (n=5 biological replicates; ***P<0.001, Student's t-test).
A, B and C. Changes in mRNA expression of Ucp1 (A), Pgc1α (B) and Pparγ(C) from WT and TRPV2KO iBAT 4 h after intraperitoneal administration (i.p., arrows) of saline or a selective β3-adrenergic receptor agonist, BRL37344 (600 µg/kg body weight). Mean ± SEM, n = 5 - 7; * P < 0.05 vs. saline group; # P < 0.01 vs. WT BRL37344 administration group. One-way ANOVA followed by 2-tailed t-test with Bonferroni correction.
B Total counts of WT donor CD4+ T cells in mice from (A) (n=13 100% WT, 8 25% WT, 14 10% WT, 6 1%, 14 0% WT). Two representative experiments shown out of 3. Mean ± SEM.
(C) The indicated plasmids of Myc-tagged wild-type NLRP3 or its mutants Y132F, Y164F, Y251F, Y570F and Y589F were respectively transfected into HEK293T cells along with GFP-tagged EphA2, and then cell lysates were immunoprecipitated with the anti-Myc antibody, followed by western blot analysis with the anti-p-Tyr antibody, anti-HA antibody and anti-Myc antibody.
Human osteosarcoma U2OS cells were pre-treated with dactinomycin (DACT), bortezomib (BTZ), daunorubicin (DAUN), docetaxel (DOC), doxorubicin (DOXO), epirubicin (EPI), mitoxantrone (MTX), paclitaxel (PACL), vinblastine (VB) and vincristine (VC) at 0.5, 1 and 5 µM ; with cisplatin (CDDP) at 75, 150 and 300 µM, with oxaliplatin (OXA) at 250, 500 and 1000 µM and with crizotinib (CRIZ) at 10, 20 and 40 µM for 1.5 to 2.5 h Cells were treated for 2.5 h and before fixation and permeabilization. Then, cells were stained with a rabbit anti-fibrillarin antibody followed by a staining with an anti-rabbit AlexaFluor-647- or AlexaFluor-546-coupled secondary antibody as well as with a mouse anti-nucleolin antibody followed by a staining with an anti-mouse AlexaFluor-488-coupled secondary antibody. Then images were acquired and colocalization between both signals was assessed (C). The surface overlap coefficient (SOC) was calculated and ranked between the untreated control (Ctr) and the positive control (DACT) Representative images of DACT 1 µM, BTZ 1 µM, CDDP 150 µM, CRIZ 20 µM, DAUN 0.5 µM, DOC 1 µM, DOXO 1 µM, EPI 1 µM, MTX 1 µM, OXA 500 µM, PACL 1 µM, VB 1 µM, VC 1 µM are shown
A. Top: Molecular architecture of tetravalent F4L5.13. Bottom: Schematic for activation of Wnt/ßcatenin signaling by F4L5.13.
Bone marrow from wild-type (Atg16L1+/+) was used to reconstitute irradiated littermate control mice (B6 WT → control [●] ) or δWD mice (B6 WT → δWD [○] ). Bone marrow from δWD mice was used to reconstitute irradiated δWD mice (δWD → δWD [▲] ). After 12 weeks, mice (n = 5 per group) were challenged with IAV X31 (103 pfu). (D) Lungs taken at 5 d.p.i. were analysed for neutrophils (Ly6G), neutrophil extracellular traps (NET; anti-H3) and macrophages (Iba-1) .
Time-lapse confocal imaging (at a rate of one image stack/min) was used to document dynamic behavior of ONL microglia in rd10 retinal explants at ages P21-24. Example in which the engulfment of photoreceptorsomata by microglial phagocytic cup was followed up by actual phagocytosis in which the engulfed cell (red *) is translocated intracellularly within the microglial cell toward the cell body. Phagocytosis of soma occurred simultaneously with "probing" of other somata by processes of the same microglial cell (yellow *).
B. Illustration outlining APEX2-catalyzed biotin-phenol labeling. An Rbd2-Flag-APEX fusion protein oxidizes biotin-phenol to biotin-phenoxyl radical that covalently labels binding partners.
E. Comparison of the position of Arp2 relative to Arp3 in the short pitch arrangement (grey Arp2), the inactive splayed arrangement (red Arp2), and the SPIN90 bound x-ray crystal structure (cyan). The short pitch arrangement of Arp2-Arp3 was modeled by overlaying subdomains 1 and 2 of Arp3 on the same subdomains in an actin subunit in the actin filament structure 3G37(Murakam ), and then superposing Arp2 from the 4JD2 structure onto the actin subunit in the short pitch position. The SPIN90-bound complex was then overlaid onto Arp3 subdomains 1 and 2 to determine the relative position of Arp2 in the SPIN90-bound complex. Blue line shows a potential trajectory of the center of mass of Arp2 when it moves from the splayed to the short pitch position
A Bacterial pathogens invade leaf tissues through stomata. B Pathogens proliferate in the extracellular space or the apoplast. C, D Virulent pathogens spread over the infection site (C) and develop disease (D). E, F Avirulent pathogens are restricted to the infection site as a result of the construction of the CASPL- and lignin-deposited structure (E) and are eventually eliminated from the infection site of the leaf (F).
(A) Experimental design. Yeast cells growing on glucose were switched to no carbon media for 30 min. Thereafter, 20 mM H2O2 was added and metabolome analyzed by LC‐MS.
(D) CP20 and OVCAR4 stable cell lines were transfected as either empty vector (EV) or pLYS1-MICU1-Flag (MICU1) and relative MICU1 levels were evaluated using immunoblotting.
C) Thermal shift stabilization of purified dimeric NHE9*-GFP in the presence of PIP2 (red) compared to PIP2-free (black). Data presented are normalized mean FSEC peak fluorescence as mean values ± data range of n = 2 technical repeats; the apparent Tm was calculated with a sigmoidal 4-parameter logistic regression function; the average ΔTm presented is calculated from n = 2 independent titrations.
A. Protein sequences were extracted from UniProt accession number BP08_BPT4 for Enterobacteria phage T4 (gp8; Bacteriophage T4) and the Pseudomonas Genome Database (TssK1; reference strain PAO1). Conserved positions are shown in black and grey background. The secondary structural elements corresponding to the 3D structure of gp8 (PDB code 1PDM) are shown above the alignment. Regions with significant sequence conservation are indicated with a corresponding block number.
F-I. Behavrioural tests of Aβ(1-42) infusion mice. (F) Schedule of behavioural tests. In first week, 8-week-old male ICR mice (n = 8 per each group) were intravenously injected with either Nec-1 (6.25 mg/kg) or vehicle (2.5% DMSO in PBS) twice. Then 5 μl of Aβ(1-42) (100 μM) aggregates or vehicle (10% DMSO in PBS) were injected in intracerebroventricular region to generate Aβ(1-42) infusion mice model. In second week, same concentrations of Nec-1 or vehicle were intravenously injected twice again.
Paraffin sections from Bouin-fixed wild type and SPPL2c-/- testis were stained with hematoxylin & eosin (H&E). Scale bars, 100 µm.
C RNAlow neoblast size in intact animals and at 48 hpa in control or TOR KD animals (n ≥ 55).
B. Representative images of growth cones of mouse DRG neurons transfected with WT or mutant constructs treated with 75 nM Sema6A-Fc and visualized with immunofluorescent staining to detect GFP (green) and phalloidin (red). Average intensity images for all different constructs are shown in grey color. Scale bar 20 µm.
(G) Hel2(1-315) polyubiquitinates eS7A but not uS10. Western blotting after an in vitro ubiquitination assay using the Hel2-(1-315) mutant and purified ribosomes containing HA-tagged uS10.
Volcano plot of differential transcription factor (TF) motif accessibility (activity) in GPR56high (turquoise) vs GPR56low (violet) samples and their corresponding adjusted p-values determined with diffTF. Highlighted are TFs whose RNA expression was also positively or negatively affected by GPR56 KD in the RNA-seq dataset.
Simulation of the PFK rate with varying ADP/(ATP+ADP) ratios. Data information: The PFK flux was simulated as single (isolated) reaction with the following fixed metabolite concentrations relevant for the kinetic rate law of the PFK PEP: 0.27 µmol/gDW; F6P: 0.91 µmol/gDW; FBP: 9.74 µmol/gDW ; total concentration ATP+ADP: 2.67 µmol/gDW.
Upper part: in resting cells (no stress), Hsp90 interacts with DYRK3 and regulates its stability and activity. Upon stress, DYRK3 dissociates from Hsp90 and partitions inside SGs, where it is protected from irreversible aggregation and degradation. During the recovery phase after stress, soluble DYRK3 associates with Hsp90 outside or at the boundary of SGs to be stabilized. Once stabilized by Hsp90, DYRK3 could autophosphorylate its activation loop to achieve full activation and trigger the disassembly of SGs, by phosphorylating yet unknown molecular targets. Active DYRK3 would then promote translation restoration. Lower part: upon treatment with GA or 17AAG, DYRK3 dissociates from Hsp90, becomes inactive and is either targeted to SC35 speckles or degraded by the 26S proteasomes. During stress, blocking the loading of DYRK3 onto Hsp90 with GA or 17AAG redirects DYRK3 to SGs or to 26S proteasomes. During the recovery phase after stress, inhibition of Hsp90 prevents the stabilization and activation of DYRK3. As a consequence, SGs do not disassemble and translation is not restored. The model only depicts the interplay between Hsp90 and DYRK3 in the regulation of SG dynamics, although other Hsp90-dependent/DYRK3-independent mechanisms may also occur.
H. Immunofluorescence images against CB1 and the Purkinje cell marker calbindin in the cerebellum of age-matched control and ASMD-affected children. Graph shows mean ± SEM intensity associated to CB1 in the Purkinje cells expressed as percentage of the values obtained in the control child (16 and 15 replicates in control and ASMD, respectively). Scale bar, 10 μm.
(c) Juxtanuclear MRs are found in Rab7- and LAMP2-positive lysosomes. U2OS cells stably expressing DsRed-Rab7 were fixed and stained for MKLP1 α-tubulin and DAPI (left panels); wild-type U2OS were stained for MKLP1 and LAMP2 (right panel). Scale bars are 10 μm. The insets are enlargements of the engulfed MRs. Scale bars are 1 μm.
A Levels of 4EBP1 protein and its phosphorylation at Serine 65 in presence of DMSO, rapamycin (100 nM) or temsirolimus (100 nM). GAPDH is showed as loading control.
E. Comparison across treatment cohorts of the relative change in baseline of Per2-driven bioluminescence when vehicle, Prok2 or VIP was applied within CT9-12. Only VIP is statistically shown to significantly raise Per2::Luciferase baseline levels (p=0.0007; vehicle vs. Prok2, ns. p=0.17; vehicle vs. VIP, **p=0.002, Prok2 vs. VIP, *p=0.02). F. The relative change in amplitude of Per2::Luciferase rhythm after treatment with Prok2 or VIP significantly decreases compared to vehicle application (p=0.002; vehicle vs. Prok2, *p=0.01, vehicle vs. VIP, **p=0.001).
Phosphorylation of Ub by PINK1 has multiple consequences. Structurally, it alters the electrostatic potential of Ub, but also generates a new UbretraCT conformation with a retracted C‐terminus. The UbretraCT conformation is in slow exchange with the common Ub conformation. Functionally, Ub phosphorylation leads to a gain‐of‐function of Ub, as it becomes an allosteric activator of Parkin. We here show that phosphoUb also has loss‐of‐function effects, as it inhibits some assembly and disassembly systems. Additionally, it is possible that phosphoUb is recognized specifically by Ub receptors.
D Oocytes expressing KCC4 were incubated with NAM for the indicated times, and KCC4 protein levels (upper panel), and activity (lower panel) were analyzed by SDS-PAGE/immunoblotting or Cl--dependent 86Rb+ uptake under hypotonic conditions.
A Close-up view of Ca2+-free MICU1-MICU2 interfaces I (left and middle) and II (right). The atomic interactions at the interface I consist of mainly electrostatic (left) and weak hydrophobic (middle) interactions, while interface II mainly contains hydrophobic interactions (right)
I: Relative mtDNA copy number in Detroit 551, WS5A and CP2A iPSCs by RT-qPCR analysis using ND1 and APP (n=5, technical replicates per clone for control; n=5, technical replicates per clone for WS5A and CP2A). Values are presented as Log2 of the ratio between the expression values of ND1 in relation to APP.
D, multiscale network of cell sub-community and coEM eigengenes depicted with a force-directed layout and edge bundling. Gold nodes, cell sub-communities; gray nodes, coEM eigengenes; large diamonds, clinical variables; red edges, positive correlations; blue edges, negative correlations. Edges are filtered to Pearson correlations significant at P < 0.001, and thickness corresponds to the square of the correlations. A cluster of sub-communities and coEMs associated with convalescence (dashed gray box) and a corresponding cluster of sub-communities and coEMs associated with acute infection (solid black box) surround the "convalescent" node. A positive correlation between convalescent anti-CHIKV antibody (Ab) titer and CD14+CD16+ monocyte sub-community 1 frequency (shown previously in Appendix Figs S3A and S3B) is also visible (asterisk and arrow).
H. Lysates from HeLa cells were subjected to ChIP assay. ChIP products were amplified by qPCR reaction with the indicated pairs of primers. Data shown are mean ± SD (n = 3; *P < 0.05, two-tailed t-test).
G Quantification of FLAG and DAPI fluorescence intensity along a line centered at the nuclear envelope. Eight OHC were measured.
Micrograph and LC3B antibody labelling of adipocytes neighboring the nerve cells of Porcellio d. dilatatus.These adipocytes are localised around the nerve cells of the CNS and constitutes the sheathing of this organ. (A) At 30 days post-injection, autolysosomes, autophagosomes but also bacteria were observed: autophagic process was already higher compared to the control (Ad: adipocyte, Ap: Autophagosomes (Autophagic hallmark), Al: Autolysosomes, Wo: Wolbachia, Arrow head: magnified area). (B) At 60 days post-injection, the adipocytes were severely damaged by the accumulation of autophagic vesicles (Ad: adipocyte, Ap: Autophagosomes, Al: Autolysosomes, Wo: Wolbachia, Arrow head: magnified area). (C) With the antibody labelling anti-LC3B, the protein LC3B implicated in autophagic processes was detected in adipocytes of P. d. dilatatus injected with wVulC at 45 days post-injection. The highly labeled spherical structures would reflect the incorporation of the LC3B protein in the phagophores. (D) With adipocytes of P. d. dilatatus injected by wDil but also in other tested situations, only really few of these structures were detected by epiflorescent microscopy.
A. Schematic of the differentiation protocol timeline. Maintenance Medium (MM) = iPSC medium (StemFlex with 1x penicillin/streptomycin), NCC differentiation medium = DMEM-F12, 10% fetal bovine serum, 1 mM sodium pyruvate, 1 mM penicillin/streptomycin, 1 mM non-essential amino acids, 110 µM 2-mercaptoethanol, 10 ng/mL epidermal growth factor.
Differential expression analysis for ACE2 expression changes in treated vs control samples was performed with the level 3 CMAP data of 24 hours response values using limma (Ritchie et al, 2015; Methods). Volcano plots showing the log fold-change (X-axis) and uncorrected negative log10P value (Y-axis) of ACE2 expression changes are given for (A) 48 antihypertensive drugs The enrichment of positive/negative ACE2 expression regulators in different drug classes based on their mechanism of action (MOA) was tested with the GSEA method as implemented in the R package fgsea (Segushichev, 2016; Methods), and the enrichment significance (negative log10 P values) is shown in bar plots in (B) , for the analysis on the 48 antihypertensive drugs CCBs, calcium channel blockers; ARBs, angiotensin II type-I receptor blockers; ACEIs, angiotensin-converting enzyme inhibitors
(D) Western blotting analyzed Il-17rb in shLacZ or shTgfbr1 4T1 cells treated with recombinant TGF-β1 for 5 days.
UMAP plot revealing the cell type annotations of three samples. B) The cellular composition of three healthy kidney samples.
E Western blot analyses showing the extent of HIF1α stabilization and steady state level of VHL protein with and without the treatment with FG4592 (100 μM) in RKO cells. GAPDH is showed as loading control.
U87 cells were incubated in DMEM (devoid of phenol red, glucose, pyruvate and glutamine) supplemented with 25 mM U-13C-glucose, 4 mM glutamine and 1.5% dialyzed FBS in the presence or absence of 20 µM LXR623 for 24 hours. Cells were then harvested for LC/MS analysis. The fractions of each different isotopologue of each metabolite were calculated (percentage of the entire pool). Shown are the isotopologues of the TCA cycle intermediates labeled by glucose carbons and non-labeled isotopologues (m+0).
J Time course of expression of WT-CD40LG mRNA or CO-CD40LG mRNA, measured as fold change (FC) on IPO8 housekeeping gene and normalized to T0. Sorted edited (+) and sorted unedited (-) CD4+ T cells were analyzed before and 3, 6, 12 hr after Actinomycin D treatment (n=1 for each group).
Representative confocal laser microscopy images of propidium iodide-stained guard cell starch granules of intact leaves of WT, stp1-1, stp4-1, stp1stp4, suc1 and suc3 plants. Scale bar, 10 µm.