EMBO/sd-character-level-ner huggingface dataset:
C. SDS-PAGE analysis of complexes purified from cell expressing deletion mutants of the pBADM11_trwN/virB1-trwE/virB10Strep_trwD/virB11_HistrwB/virD4 constructs termed pBADM11_ΔtrwX/ΔvirBY (see main text). The same molecular weights marker has been used on this gel as in the gel presented in Figure 1A. * indicates degradation products of TrwK/VirB4.
Confocal microscopy images of seeds 3 DAP. Endosperm and embryo morphology in cycb1 double (B) mutants. Magenta arrowheads indicate enlarged endosperm nuclei, while green arrowheads indicate atypical agglomerates of endosperm nuclei. Scale bars: 25 μm.
C: Principal component analysis comparing cancer (HGG and LGG) and control samples (healthy and other CNS diseases) using data from the urine fragmentation features. Red arrows indicate features tested during the predictive analysis.
(C) qPCR gene expression analysis of inflammatory genes Il-1β, Tnf, Il-6, iNos and iκbα by qPCR in mixed cortical cultures (left; in vitro) incubated with EVs isolated from CSF from untreated (black) or LPS treated (grey) mice and in brain tissue (right; in vivo) before (black) and 8 h after LPS injection (grey) (n=3).
F) Gene expression analysis by RT-qPCR of CrizR1 cells treated with the indicated concentrations of bemcentinib for 48h. LOX: P=0.03; SNAI2: P =0.02; VIM: P =0.03.
C, Confocal image of endo-GFP-ORP2 and pFAK immunofluorescence staining in saponin pre-permeabilized cells loaded with LDL for 2 h before fixation. GFP antibody was used to enhance endo-GFP-ORP2 signal. Insets show examples of "no contact", "contact" and "overlap" of organelles. Dashed line indicates cell edge. D, Quantification of pFAK, integrin β1, and NPC1 association with endo-GFP-ORP2 in C. n = 380 pFAK; 353 integrin β1; 232 NPC1 organelles in 2 cells.
D. Relative levels of mtDNA of Fbxl4 knockout (-/-) embryos and the corresponding wild type (+/+) embryos at E13.5. Data represent mean ± SEM, n=5. Student's t-test; *, p<0.05.
A: Serial dilutions of stationary phase cultures of the indicated strains were spotted on YEPD and incubated at 25°C and 34°C.
Statistical analysis of the expression levels of TAPBPL on tumor tissues. The data were presented as relative expression levels of TAPBPL on tumor tissues versus relative normal tissues (each group was normalized with isotype Ab first) (n=5). Significance was calculated by two‐tailed Student's t‐test. * P<0.05 compared with normal tissue. (E, F) Analysis of TAPBPL protein expression on the indicated cancer cell lines. Representative flow cytometric profiles and (F) statistical analysis showing the expression levels of TAPBPL protein on the cancer cells (n=3). Significance was calculated by two‐tailed Student's t‐test. * P<0.05 compared with isotype Ab.
Confocal z-projections of MARCM neuroblast (NB, A-F) and single-cell (SC, G-L) clones labeled with membrane bound GFP (mCD8-GFP; CD8) driven by the γ specific Gal4 driver GMR71G10-Gal4 (γ-Gal4). At L3, NB and SC clones expressing dpr12 RNAi are similar to equivalent WT clones (A; n=20/20, D; n=15/15, G; n=15/15 and J; n=17/17). At 48hr APF and adult stage, WT NB (B; n=15/15, C; n=10/10) and SC (H; n=16/16, I; n=13/13) clones extend their axons to form the full adult lobe. In contrast, clones expressing dpr12 RNAi (E; n=14/14, F; n=22/2, K; n=18/24, L; n=19/27) fail to extend their axons to the distal part of the medial lobe (asterisks). I' and L' are traces of multiple single-cell clones depicting each cell in a different color.
(C) Sprouting of WT and EVL-/- primary MLEC spheres in the absence (Basal) or presence of VEGF (50 ng/ml); asterisks indicate sprouts; scale bars, 100 µm.
D qRT-PCR analysis (PrimePCRTM Assay) of different cyto-/chemokines in B16F1 WT cells plotted vs B16F1-XIAPKO cells (clone1 and 2). Samples that are at least 2-fold up-regulated are shown in red, samples that are at least 2-fold down-regulated are shown in green.
(h) Confocal micrographs of Hela cells as in g were transfected with PARKIN-YFP (green) plasmid before CCCP treatment, then (i) treated with CCCP for 12 h. Mitochondria were stained with anti-Tomm20 (red) 4',6-diamidino-2-phenylindole stained nucleus was shown in blue. Co-localization was indicated by white colour. Scale bar=10 μm. (j) Quantification of the co-localization percentage of Tomm20 (red) with parkin (green) per cell by Imaris software (n=7 for NS and PGAM5 shRNA group separately. Results are presented as mean and s.d. values and were analysed by the student t-test). All the blots and images are representative of three independent experiments. DMSO, dimethylsulphoxide.
Shown is the common tree of bacteria and archaea as represented in the NCBI Taxonomy resource (). Organisms in which a BREX system exists are colored; color code follows the BREX subtype coloring from Fig . Extensive horizontal transfer is observed by the lack of coherence between the species tree and the PglZ phylogeny.
Tissue microarrays (TMAs) from primary PCa (n=132) and CRPC (n=148) were stained via immunohistochemistry for poly(ADP-ribose) (PAR), and scored by a clinical pathologist (T. Parsons) for intensity (0-3) and percentage (0-3) PAR score was generated via the equation: (intensity x 1) + (percentage x 2). PAR scores were compared between primary and CRPC. ****=p value<0.0001 by Chi-square test
F The mesenchymal marker fibronectin 1 (FN1) is induced following TGFβ stimulation.
Signalling downstream of VEGF-A/VEGFR2 assessed in HDMEC, untreated (NT, non-transfected), transfected with non-targeting siRNA (c/cntrl), or with two different PALD1-targeting siRNAs (KD#1 and KD#2), and treated with VEGF-A for 0-10 and 0-20 min, respectively. Immunoblotting of cell lysates for phosphorylated Erk1/2 (pT202 and pY204), and total Erk. Actin served as loading control c). PALD1 knockdown was verified by blotting for Paladin. Quantification of pErk1/2 (normalized to total Erk1/2) (d). Mean±SEM, two-way ANOVA, n=3 biological replicates. Data information: *p < 0.05, **p < 0.01.
C. hPBT cells were transfected with mtYFP and after 24h AICD was induced. Representative reconstructions of confocal z-stacks of the mtYFP fluorescence 30' after AICD induction is shown. Scale bar, 5μm.
Immunoblot of c-myc and myogenin (L in C2C12 myocytes transfected with mGPDH plasmid with the AMPK inhibitor CC at 24 h (L,M after differentiation
Schematic diagram showing serial deletions of GID1. GID1 fragments were expressed in E. coli and used for defining the PA binding region. CD1/2 denote conserved domain HGG and GXSXG. Catalytic triad including three conserved amino acids of GID1, S, D, and H (vertical red bars).
Phase separation over time as monitored by turbidity of 50 μM MBP-N in 50 mM Tris pH 7.4 after addition of TEV protease A) with varying torula yeast RNA (at 100 mM NaCl) or B) varying NaCl concentrations (at constant RNA concentration). Error bars represent standard deviation of three replicates.
(B-C) Cumulative distributions of (C) molecular weights for three different metabolic groups. All distributions were significantly different with p < 0.05 using a non-parametric Wilcoxon Rank-Sum test (Appendix Table S4).
E Seedlings were grown for 7 days in W and then transferred to total darkness for several days to induce senescence, as illustrated at the right panel.
Control, M1 (LPS stimulated) and M2 (IL-4 stimulated) RAW 264.7 cells, as well as NIH 3T3 cells were treated with TGFβ (30 ng/ml), or TGFβ + 2G8 (100 ng/ml) for 24 hours. Conditioned media (CM) was collected mouse IL-6 ELISA (B-C).
RT-qPCR analysis of FAM214A mRNA splicing. Intron-retaining isoforms (IR) of the FAM214A pre-mRNA are illustrated above. The retained intron is indicated by a red line. Arrows indicate the positions of the PCR primers used. The graphs show the relative amounts of the IR (left) and spliced (right) forms in control and HSATIII KD cells under three conditions: 37°C, 42°C for 2 h, and 42°C for 2 h followed by recovery at 37°C for 1 h (recovery). Expression levels were calculated as the ratio of each RNA to GAPDH mRNA and were normalized to the levels in control cells under normal conditions (37°C). Data are shown as the mean ± SD (n=3); p-values (p<0.05, Sidak's multiple comparisons tests) are shown above.
G-protein-coupling preference and phospho-site patterns in the carboxyl-terminus of V2R and B2R, deduced based on a previous study (Zhou et al., 2017). The phospho-site patterns in the form of PXPXXP and PXXPXXP are underlined and color-coded. Both, V2R and B2R recruit βarrs in "class B" pattern (Oakley et al., 2000) as reflected by stable interaction and endosomal trafficking of the receptor-βarr complexes.
I Phylogenetic analysis of all known human SPRR coding-sequences (cds by means of a maximum likelihood approach. The length of the horizontal bar indicates 0.05 mutations/site. Sequence similarity suggests a common ancestor of all SPRRs, but a distinct composition of SPRR5.
A, B Unmethylated (WT-C) and hydroxymethylated (WT-hmC) I3-I7 clones were transfected with siRNA against Tet1 and Tet2 (siTet1/2) or non-target siRNA (siNT). qRT-PCR (A) and Western Blot (B) confirmed knockdown efficiency relative to CHO GAPDH and the p84 loading control, respectively.
(c) mRNA for the indicated genes in epididymal white adipose tissue (eWAT) (n=4)
(A) A subset of exclusive ATM-dependent sites in WT cells, which responded to neocarzinostatin (NCS) also in A-T cells. Their dependencies in A-T cells are shown. (B) Dependencies of S/TQ phosphorylations within the same subset.
(f) Percent survival of 15 d old plants with and without SA187 under NHS, HS and LAT conditions. Data information: percent survival measuremts after recovery at 22°C for 4 days. For percent survival, plants with green leaves were scored as live plant out of 12 plants for each biological repeat in different temperature treatments. All treatments are compared with direct 44°C heat stressed plants. Plots represent the mean of 3 biological replicates bars representSE Asterisks indicate a statistical difference based on the Mann-Whitney test (* P < 0.05 )
B VHIO179 PDTXs were grafted into CB17-SCID female mice. Pyridostatin was administered intravenously (7.5 mg/kg/day) over the indicated periods of time. Vertical dotted line indicates end of treatment. Tumour volume was measured at the timepoints shown on the graph and expressed relative to tumour volume at the beginning of treatment. Each experimental group included n = 7 mice. Error bars represent SEM. P values were calculated between treated and untreated tumours at day 24, using an unpaired two-tailed t-test. ****, P ≤ 0.0001.
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. F) AGR2 dimerization was monitored with ERMIT (wild-type (WT)). The luminescence signal was abrogated when using the kinase dead (KD) constructs and by the constructs exhibiting mutations in the dimerization domain (E60A or C81S or double mutant (DM)). The graph represents average signal normalized on reporter protein expression ± SD (n=5; **: WT/KD (p=0.002), E60/WT (p=0.0034), E60/KD (p=0.001), C81/KD (p=0.004), DM/WT (p=0.0021) and DM/KD (p=0.0017), respectively; *: C81/WT (p=0.0098)).
SNX10 conditional knockout (SNX10 cKO) mice with or without IL-10 KO background and littermate wild type (WT) mice with or without IL-10 KO background were compared (n = 6 animals, each group). G The content of TNF-α, IL-6, IL-12/IL-23 p40 and IL-17A in the serum of WT, SNX10 cKO, IL-10 KO and SNX10 cKO IL-10 KO mice at the 16th week were measured by ELISA. Data information: data are means ± SD. One-way ANOVA followed by Bonferroni post hoc test was used for statistical analyzes. *p < 0.05; **p < 0.01; ***p < 0.001.
Figure 6. Refined transport mechanism of ABC exporter McjD based on structural, biochemical and biophysical data. A, B) Binding of ATP alone (futile cycle) is not coupled to an opening of the TMD that remains occluded. NBDs can close in the presence of ATP and do not require substrate for closure. On the other hand, the NBDs are more dynamic and they can sample a nearly closed dimer that is driven to full closure in the presence of ATP. Binding of both ATP and MccJ25 are coupled to open up the TMD, which reverts back to an occluded conformation upon substrate release. ATP hydrolysis and ADP release resets the transporter in an inward conformation for a new transport cycle. Expanded View Figure Legends
(A) Top: Rose plot visualizing the acrophases (based on rhythmic genes in the liver transcriptome from (Atger et al., 2015)) of genes exhibiting heat-induced (orange, n=797) and cold-induced (blue, n=828) upregulation of GE in mouse hepatocytes, respectively. Bottom: Acrophases of genes with cold-induced (blue, n=55) and heat-induced (orange, n=47) poison exon events, respectively. Numbers indicate respective ZT, with the left half representing night (at which mice are active and have an elevated body temperature) and the right half representing day (at which mice are asleep with lower body temperature). The black circles represent expected normal distribution if data would be randomly sampled.
(F), (G) p53 knock-out does not rescue Parn-/-. No Parn-/- p53-/- mouse was born from various combinations of Parn+/- and either p53+/- or p53-/- crosses (49 and 56 pups, respectively). Statistical significance (P = 0.000886) of the differences between the observed and expected genotype distributions was assessed by χ2-test.
(C) Single confocal sections of HeLa cells transfected with a vector expressing myc-SseL for 16 h followed by treatment with puromycin (5 µg/ml) for 4 h and immunolabelled with anti-myc (blue), anti-p62 (green) and anti-ubiquitin (Ub, red) (scale bars, 5 µm). The lower panels show a merged image of p62, ubiquitin and myc-SseL. Arrows indicate ubiquitin and p62 aggregates present in untransfected cells and arrowheads indicate cells expressing myc-SseL
C) Color coded radial kymographs of divergence for a representative movie. Low divergences are blue, high are red (see scales). Note the overall positive divergence in the nests and negative in the LECs.
The graphs depict the recovery of CAR1-mcherry (left) and tPH-CynA-KikGR (right). Mean ± SEM is shown for n = 2 cells.
A-D Immunoblotting using an anti-P-Akt, anti-P-S6, anti-4EB-P1 or anti-GAPDH (loading control) antibody of protein extracts from CAFs pre-treated (+) or not overnight with PTX (100 ng/ml) (A), gallein (10 μM) (B), NSC87877 (10 μM) (C), Src inhibitor (5 μM) (D), treated (+) or not with SOM230 (10−7 M) for 30 min (representative of n = 3).
(E) 293 cells were co‐transfected with GFP‐S‐Ubqln1 and HA‐Ubqln4, HA‐Ubqln4 ΔUBA or HA‐Ubqln4 ΔUBA I55A (I55 in the UBL domain of Ubqln4 was mutated to A). GFP was immunoprecipitated and analysed by western blot using anti‐GFP and anti‐HA antibodies.
(E) qPCR analysis of Streptavidin RIPs of circHIPK3 or GAPDH enrichment in HEK-293T cells transfected with either biotinylated miR-29b or miR-30c over scr (n=4). Data information: data are presented as mean ± SD. *P<0.05, **P<0.01, ***P<0.001 (Unpaired Student's t-test). All repeats are biological.
C. Homology model of TetB using YajR (PDB 3wdo) built using Phyre2 where the periplasmic side is on top and the cytoplasmic side is on the bottom. The A-helices are shown in blue, B-helices are shown in green, C-helices are shown in grey and the interdomain loop is cyan. Spheres indicating variant positions were made using PyMOL (K183 and A290V- red; F151 and F179- red; and T326-black as this residue is altered in variant 6 and 7). The right image depicts the view through central TetB pore from the periplasm into the cytoplasm.
(A Representative image and quantification of the number of PML NBs in HIV-1 DNA+ vs mock infected CD4+ T-cells. Scale bars = 2μm. Infected cells were identified with DNA FISH and PML NBs were stained by IF.
A. spMis18fl-Myc co-immunoprecipitates with both GFP-tagged spMis18fl and spMis18MeDiY, but shows reduced association when MeDiY-mediated dimerization is disrupted in spMis18flI31A. The asterisk (*) in the top panel denotes the IgG heavy chain.
(A-G) Ablation of Sst-Cre::AviliDTR positive sensory neurons by injection of diphtheria toxin (DTX). Immunostaining of DRG from Sst-Cre::AviliDTRmice with an antibody against the diphtheria toxin receptor and IB4 in the absence of diphtheria toxin (A-C) and after systemic injection of diphtheria toxin (D-F).
(F) ELISA analysis of IL8 in supernatants of HEK293T NOD1/2 KO cells transfected with indicated NOD1 or NOD2 mutants. After 24 h transfection, cells were stimulated with S1P (20 µM), iE-DAP (20 µM) or MDP (20 µM) together with digitonin for 20 h.
F, Schematic outline for plasma membrane D4H labeling in combination with ORP2 degron system, and representative widefield epifluorescent images of co-plated cells after 4 h of LDL loading. Asterisk indicates ORP2-depleted degron cells. Dashed lines separate ORP2 expressing and depleted cells. G, Quantification of F. Mean ± SD, n = 20 fields of cells pooled from 2 independent experiments. Student's t-test.
A. Deconvolved inverted fluorescent micrographs of the indicated strains expressing Chm7-GFP (percentages ± SD of the proportion of cells with Chm7-GFP foci is at bottom of each panel, see Figure EV5B). Scale bar is 5 μm.
D) Hemocytes from WL OregonR infested by wasp. The immunolabelling was done with antibodies targeting the new lamellocyte markers identified in this study Rhea (in gray, top panels) and Shot (in gray, lower panels). Phalloidin-FITC (in green) labels the actin filament particularly abundant in lamellocytes (Tokusumi et al., 2009) and the nuclei were marked with DAPI (blue). Full stacks are displayed, the left panels show the overlay of DAPI, FITC and the lamellocyte markers, the middle panels show the FITC alone and the right panels the lamellocyte markers alone. The scale bars represent 20µm.
U87 cells were treated with DMSO or LXR623 20 µM with the indicated time point. Thereafter, whole cell protein lysates were collected and subjected to standard western blot for the expression of the respiratory complexes (OXPHOS), Noxa, and ATF4. A star indicates an unspecific band.
D Steady state levels of mitophagy related proteins VDAC1, p62 and LC3-II in control and TIMM50 mutant fibroblasts growing in either glucose or galactose were assessed by Western blot using GAPDH as internal control. E Quantification of the steady state levels of VDAC1, p62 and LC3-II in control and TIMM50 mutant fibroblasts growing in either glucose or galactose. Data are shown as mean ± SD, n = 4 biological replicates; ∗∗p < 0.01, ∗*∗p < 0.001 grouping both controls together.
(C) Extracts from liver tissues of wild-type mice were immunoprecipitated with antibodies against Ing5 followed by immunoblotting with the antibodies against the indicated proteins.
Untreated and activated pΦ from C57BL/6 mice were infected and intracellular bacillary survival was monitored 96 h p.i. Data is presented as mean CFU log10/ml ± SEM and is representative of two biologically independent experiments, each performed in triplicates (n=3). pΦ isolated from indicated genotypes were activated, and either left untreated or treated with NO inhibitor, 1400W. Intracellular bacillary survival was monitored 96 h p.i. Data is presented as mean CFU log10/ml ± SEM and is representative of two biologically independent experiments, each performed in triplicates (n=3).
(A) NuMA structure upon microtubule depolymerization. Nocodazole-treated HCT116 CMV-OsTIR1 CEP152-mClover-mAID cells were treated with 100 ng/ml nocodazole. Gray, red, green and blue represent α-tubulin, NuMA, CEP152 (mClover) and DNA, respectively. Scale bar, 5 μm.
(b) EGFR degradation. HCT116.Vec, HCT116.UVRAG and HCT116.UVRAGΔN(1-147) cells were treated with EGF (200 ng ml−1) at 37 °C for the indicated times. WCLs were subjected to immunoblotting with an anti-EGFR antibody. EGFR at each time point was quantified and indicated as a percentage relative to that at time zero (right panel; data are mean ± s.e.m., n = 3).
B. Bar graphs showing the markedly different reversal potentials of PC2_AA channel and the PC1-CTF/PC2_AA channel in bath solutions containing 100 mM of the indicated ions. Oocyte numbers are indicated in parentheses. Data are presented as mean ± SD (n.s.: not significant, ***P < 0.001, Student's t-test).
(A) DDL-N but not DDL-C associates with PARP2. FLAG-tagged DDL-N or DDL-C was co-expressed with PARP2-HA in protoplasts for Co-IP assay. Protoplasts were treated without or with 100 nM flg22 for 30 min.
2-DOG assay to monitor for loss of GAL1 function from tetraploid strain RBY18 after culture on SCD medium with or without PQT (600 μg/mL), H2O2 (2 mM), or PL (100 μg/mL) at 37°C for 7 d.
(A) Schematic of network analysis to identify TFs with activity (increased or decreased) in controlling the transcriptional state of MTB during infection of host cells. Abbreviations: dec; decreased, inc; increased.
F) Immunoprecipitation of the Mpl‐Jak2 complex in different cell lines analyzed by immunoblotting with anti‐Mpl and anti‐JAK2 antibodies.
(F) Enrichment of the gene modules identified in (E) for independent gene sets previously established from the analysis of other microarray datasets (blue font), belonging to specific signaling pathways (red font), associated to specific functions or diseases (violet font) or regulated by the indicated upstream regulators (black font), as assessed by using Ingenuity Pathway Analysis (IPA). Data are represented as a heatmap, with gene modules identified in panel E as columns and gene sets as rows. The colored cells indicate the significance of the enrichment of each gene module for each gene set, as computed by IPA analysis and according to the color scale shown below the heatmap
12-month-old IBA-1 stained RPE flatmounts of Cx3cr1GFP/GFP (H) and Cx3cr1GFP/GFPApoE−/− (I) mice.Quantification of subretinal IBA-1+ mononuclear phagocytes in 2-month-old (left) and 12-month-old (right) mice of the indicated strains (n = 9-20/group ANOVA/Dunnett test at 12 months: Cx3cr1GFP/GFP versus any other group *P < 0.0001; Mann-Whitney U-test at 12 months of Cx3cr1GFP/GFP versus Cx3cr1GFP/GFPApoE−/− *P < 0.0001).
(B) Exome analysis showing the biallelic changes c. 1348_1349del and c.555 +1G>A. Red arrow points to the place of mutation. Orange and green boxes indicate the reference nucleotide and its substitution, respectively.
(D) Stereological analysis of cortical area covered by Congo Red-positive plaques in male (n=10) and female (n=8) APP23 mice (left) and representative images (right), scale bar = 500 µm. Mean ± s.e.m., statistical analysis: two-tailed unpaired t-test, ***p=0.0001.
C Histogram represents fusion index quantification. At least 7 randomly chosen microscope fields of two independent biological samples were analysed (n=2). Data are presented as mean ± SD of the biological replicates.
A MOAP-1 downregulates the levels of the diethylnitrosamine (DEN)-induced p62 bodies in a time-dependent manner. LO2 cells were transfected with plasmid encoding Myc-MOAP-1. 14 hours later, cells were treated with DEN (200 µM) for the indicated period of times, before being subjected to IF with anti-Myc (in green) and anti-p62 (in red) antibodies. Cells expressing Myc-MOAP-1 were marked by dashed lines. Data information: nuclei were counterstained with DAPI (blue)
(c) Representative confocal images of colocalization of GFP with the lysosome marker LAMP-1 in COS-7 cells transfected with either WT-GFP (n = 17) or CTM-GFP (n = 16). Scale bar, 20 μm.
C) Structure of BID (PDB:2BID) depicting cancer-related residues localized at α-helix 6 in blue.
(B) Western blot analysis of FLIP, Caspase 8 and FADD in the soluble unbound fraction
(A) Schematic of domain distribution of wildtype human ArfGAP1 (amino acids 1-406) and the COPI defective mutant of ArfGAP1 (amino acids 1-394). Critical residues of various domains are highlighted.
(E) The level of malonylated mDia2. Equal amount of immunoprecipitated mDia2 either from TFAM knockdown or control cells was loaded in Western blot assay.