EMBO/sd-character-level-ner huggingface dataset:
Figure 3A, B The period of DD locomotor rhythm of Nipped-A RNAi flies over-expressing tim (A) or carrying heterozygous tim01 mutation (B). Ptim is a tim cDNA construct driven by tim promoter. Data information: Error bars represent SEM. Digits on the bar are the number of flies tested. Percentage of rhythmicity is indicated above the bars. Statistical difference is measured using one-way ANOVA, P<0.001, Tukey's multiple comparison test, *P<0.05, **P<0.01, ***/###/+++/$$$P<0.001, * compared with the G4 control, # compared with the UAS control, + compared with the Nipped-A RNAi flies, $ compared with the over-expression or mutant flies. White bar indicates UAS or GAL4 controls. Dashed bar indicates flies with genetically manipulated core clock gene. Gray bar indicates flies with Nipped-A knocked down. Checked bar indicates flies with both genetically manipulated core clock gene and Nipped-A knocked down. G4, GAL4; U, UAS. C, D The period of DD locomotor rhythm of Nipped-A RNAi flies over-expressing Pdp1ε (C) or carrying heterozygous Pdp1ε3135 mutation (D). Data information: Error bars represent SEM. Digits on the bar are the number of flies tested. Percentage of rhythmicity is indicated above the bars. Statistical difference is measured using one-way ANOVA, P<0.001, Tukey's multiple comparison test, *P<0.05, **P<0.01, ***/###/+++/$$$P<0.001, * compared with the G4 control, # compared with the UAS control, + compared with the Nipped-A RNAi flies, $ compared with the over-expression or mutant flies. White bar indicates UAS or GAL4 controls. Dashed bar indicates flies with genetically manipulated core clock gene. Gray bar indicates flies with Nipped-A knocked down. Checked bar indicates flies with both genetically manipulated core clock gene and Nipped-A knocked down. G4, GAL4; U, UAS. E, F The period of DD locomotor rhythm of Nipped-A RNAi flies over-expressing per (E) or carrying perL mutation (F). Data information: Error bars represent SEM. Digits on the bar are the number of flies tested. Percentage of rhythmicity is indicated above the bars. Statistical difference is measured using one-way ANOVA, P<0.001, Tukey's multiple comparison test, *P<0.05, **P<0.01, ***/###/+++/$$$P<0.001, * compared with the G4 control, # compared with the UAS control, + compared with the Nipped-A RNAi flies, $ compared with the over-expression or mutant flies. White bar indicates UAS or GAL4 controls. Dashed bar indicates flies with genetically manipulated core clock gene. Gray bar indicates flies with Nipped-A knocked down. Checked bar indicates flies with both genetically manipulated core clock gene and Nipped-A knocked down. G4, GAL4; U, UAS.
Figure 5A. Spermatocytes were immunolabeled against TACC3 (green), SYCP3 (red), CETN3 (magenta), and stained with DAPI (blue). Zoom images of the centrosomes are presented to the right. Scale bars = 5 μm. B. Quantification of TACC3 positive centrosomes per metaphase I spermatocyte. Immunolabeling was performed on three biological replicates, with ≥20 spermatocytes quantified per replicate. The total number of cells quantified for control, Aurka cKO, Plk1 cHet, and Plk1 cKO mice were 97, 103, 96, and 105, respectively. Western blots of TACC3 from protein extracts obtained from 19dpp and 22dpp control, Aurka cKO, and Plk1 cKO spermatocytes (D). Total protein stained with 2,2,2-Trichloroethanol (TCE) display protein loading. Western blots of TACC3 from Protein extracts from control and Plk1 cHet spermatocytes at 16, 19 and 22 dpp (C). Total protein stained with 2,2,2-Trichloroethanol (TCE) display protein loading. E, F. Spermatocytes were immunolabeled against beta-catenin (green), SYCP3 (red), PCNT (magenta), and stained with DAPI (blue). Middle columns emphasize beta-catenin signal in diplonema and diakinesis spermatocytes. Scale bars = 5 μm. G. Quantification of beta-catenin positive centrosomes per spermatocyte at diakinesis. Immunolabeling was performed on three biological replicates, with ≥20 spermatocytes quantified per replicate. The total number of cells quantified for control, Aurka cKO, Plk1 cHet, and Plk1 cKO mice were 89, 106, 122, and 93, respectively.
Figure 6A. MTT assay for IGRs treated with DMSO or NB-360 (25µM). Biological replicates N=4 biological replicates. T-test analysis ** = p-value<0.01, *** p-value <0.001. Data are mean ±SD. B. MTT assay for IGRs cells treated with DMSO or inhibitor 3I (3µM). Biological replicates N=3 biological replicates. T-test analysis ** = p-value<0.01. Data are mean ±SD. C-D. MTT assay of IGRs treated with NB-360 (25µM) and different concentration of doxorubicin as indicated. Biological replicates N=4 biological replicates. T-test analysis: * = 0.01<p-value<0.05, ** = p-value<0.01. Data are mean ±SD. E. T-test analysis of IC50 values for doxorubicin used alone or in combination with NB-360 (combo). Data are mean ±SD. T-test analysis: * = 0.01<p-value<0.05; ** = 0.001<p-value<0.01.
Figure 1(A) Drawings of the nestinCreERT2 (Imayoshi et al., 2008), ROSA26rtTA-flox (Belteki et al., 2005) and tet4D-RFP (Nonaka-Kinoshita et al., 2013) alleles of the 4D line. (B) From top to bottom: experimental design of 4D induction, fluorescence pictures of the SVZ of a 4D+ mouse and quantification of the proportion of RFP- (black) and RFP+ (red) progenitors among B1, C and A cells identified with markers as indicated. (C) From top to bottom: experimental design, fluorescence pictures of the SVZ of a 4D- (left) and 4D+ (right and insets magnified) mice and quantification of the proportion of BrdU+ among B1, C and A cells (identified as in B). Note that in 4D+ mice quantification was restricted to the RFP+ subpopulation (red bars). (D) Quantification of the absolute number of B1, C and A cells (identified as in B) in the SVZ of 4D- (white) and 4D+ (black) mice regardless of RFP expression (RFP+/-).
Figure 2a. Relative abundances of cell types identified by Seurat v4 reference mapping as in Figure 1a in IPT CSF compared to control or MS patient-derived CSF. Boxplot depicting 25th-75th percentiles with median shown as central band and whiskers extending from minimum to maximum values. b. TCR repertoire of IPT CSF as analyzed by single-cell VDJ sequencing. Top, all sequenced and paired TCR clonotypes shown, clonotypes ordered counterclockwise according to abundance. Bottom, clonotype frequency stratified by T cell subset. c. Feature plot of UMAP of single cells from pseudotumor CSF shown in Figure 1a, depicting cell-wise representations of indicated transcripts. Relative expression shown. d. Heatmap of cell-cell interaction analysis depicting top predicted interactions based on receptor-ligand co-expression and reference-based cell subsets. Interaction z-score shown. e. Dot plot representation of top 30 receptor-ligand interactions based on molecule co-expression and reference-based cell subsets. Mean relative expression of both interaction partners (dot colour) and interaction p-value (dot size) shown. P-values are derived from one-sided permutation tests and refer to the enrichment of the interacting ligand-receptor pair in each of the interacting pairs of cell types. f. Relative expression of CD40, CD74, and CCL5 on indicated combined meta-clusters classified by reference-based cell identification as shown in Figure 1a. g. Circos plot representation of highlighted cell-cell interactions in IPT CSF between indicated cell subsets. Colored receptor-ligand interaction pairs from (e-f).
Figure 7(A) Absolute bacterial counts (CFUs) in human lung epithelial A549 cells 1 h after infection with MTB pre-incubated with purified serum IgA (left) or IgG (right) antibodies from TB patients (TB) compared to HD as indicated. Mean and SEM are indicated. Data are representative of three independent experiments with three technical replicates each. (B) Direct comparison of purified serum IgA and IgG antibodies on epithelial cell invasion as measured in (A). P-value was determined using Wilcoxon-Mann-Whitney test; ****p<0.0001.
protein.Figure 5(A) Primary B cells were stained with cell trace violet before they were infected, and cell cultures were started. Loss of the fluorescent cell tracking dye was recorded by flow cytometry to monitor proliferation on day 0, 4 and 6 post-infection. Mean values for 3 biological replicates, standard deviation and significance of changes in signal loss of mutants compared to wild-type controls (B) Long-term growth transformed B cell cultures infected with recombinant EBV mutants were seeded at a starting concentration of 2 x 105 cells per ml. (C) Expression of EBNA2, LMP1, PLK1, MYC, and GAPDH was analyzed by Western blotting and immunostaining of whole cell extracts of cell lines established from 3 individual donors.
CD21− pDCs get infected by EBV through viral binding to HLA‐DR.Figure 2(A) CD21 expression was evaluated by flow cytometry analysis on freshly isolated pDCs and B cells. (B) EBV infection was monitored by flow cytometry at the indicated time points. The percentage of EBV‐GFP+ pDCs is reported in each gate. (C) Surface expression of HLA‐DR on freshly isolated pDCs as evaluated by flow cytometry analysis. (A-C) Data shown are from one experiment representative of three performed. (D)pDCs were infected by‐GFP for 6 days in the presence or absence of a 30 min pretreatment with an anti‐HLA‐DR blocking Ab and viral entry and infection were monitored by confocal microscopy. Scale bar: 5 μm. Data shown are representative of three experiments performed. (E) pDCs were cultured as above and after 6 days of EBV infection, the number of GFP+ cells was counted and expressed as percentage (%) of infection. Data are shown as mean ± SEM of 20 fields pooled from two experiments. (F) pDCs were pretreated for 30 min with an anti−HLA−DR blocking Ab and then infected with EBV for 24 h. IFN−α release was tested in the culture supernatants by ELISA and data are shown as mean ± SEM of data pooled from three independent experiments. *p = 0.03, Student's t−test.
Figure 3Fluorescence spectroscopy analyses of the interaction between β-catenin and KRAS using purified recombinant proteins, intact β-catenin and KRAS. Molar ratios of β-catenin and KRAS are presented. A.U., absorbance units Nuclear magnetic resonance (NMR) titration for 15N-labeled KRAS (full-length, 1-188) with β-catenin (C-terminal fragment, 661-781). The titration points are indicated in red (1:0), green (1:5), and blue (1:10). A gradual perturbation in chemical shift is indicated by the arrow A molecular docking model for NMR spectra data represented by a ribbon diagram (left panels of C and D) and structure-based surface area (right panels of C and D) of KRAS (C; chemical shift residues, red; phosphorylation sites T144/T148, green; GTP/GDP loading site, blue). The α-interface area is presented as yellow (D) E The interface (red circle) for interaction between C-terminal domain of β-catenin (helix C) and α-interface of KRAS represented by a ribbon diagram
Pilot experiments towards first mechanistic insight.Figure 5(A) FXR1 expression in PBMC of individuals carrying the rs2601 GG (low risk; N=16) versus AA genotype (high risk; N=27). (B) PBMC microRNA expression was normalized and data is plotted from all 4 miR-181-5p members (miR-181a, b, c, d-5p). (C) Sequence homology of all 4 human mature miR-181 species shown together with sequences in the broader fragile X gene family containing binding sites for the miR-181 family (seed matches identified using Target Scan Human and SFOLD). The red letters specify seed sequences and seed matches, respectively. Chromosome positions for each seed sequence and seed match are denoted (human genome assembly GRCh38/hg38). (D) Denoted are ΔΔG values for binding of each of the miR-181 family members to different 3'UTR positions. Positions were identified using Target Scan Human and SFOLD and then processed using PITA algorithm to yield the denoted ΔΔG values. ΔΔG is an energetic score, and the more negative its value, the stronger is the expected binding of the microRNA to the given site
Figure 6A-C. Carfilzomib shrinks tumor through modulating tumor microenvironment. EG7 cells were inoculated in wild-type or Rag1-/- mice to allow tumor xenograft to reach a volume of around 80 mm3. Mice were randomized for treatment (n = 6) by saline or Carfilzomib for two weeks. Tumor growth was monitored (A) and the xenografts were dissected to photograph (B) or weigh (C) after treatment. Data are shown as mean ±SD and n indicates the number of biological replicates. *p < 0.05, ***p < 0.001 (student's t-test). D. CD4+ and CD8+ T cells play a role in mediating cancer-shrinking effect of Carfilzomib. Lung-cancer-bearing TD mice were treated by saline, Carfilzomib, anti-mouse CD4 antibody (ip.), anti-mouse CD8 antibody (ip.), or Carfilzomib plus anti-mouse CD4/8 antibody. CT scanning was performed after two-week treatment. E. Representative images of H&E staining of the treated lung tissues. Expression of Ki-67 in lung tissues was detected by immunohistochemistry method. F. Carfilzomib synergized with PD1 antibody in shrinking lung cancers. Lung cancer bearing TD mice were treated by saline, anti-PD1 antibody (ip), Carfilzomib, or Carfilzomib plus anti-PD1 (ip). CT scanning was performed after two-week treatment. G. Representative images of H&E staining of the lung tissues. Expression of Ki-67 in lung tissue was detected by immunohistochemistry method. H. Carfilzomib synergized with PD1 antibody in shrinking lung cancer through activating T cells. Treated TD mice were euthanized and the lung tissues were dissected to analyze the expression of CD69 and CD25 in CD8+ T cells by flow cytometry. I. Statistics about the proportion of CD25 or CD69 positive cells in CD8+ T cells. Data are means ± SD of three independent experiments. *p < 0.05, **p < 0.01 (student's t-test).
Sept2 is required for efficient recruitment of Drp1 to mitochondria.Figure 5(A) Immunofluorescence microscopy of Sept2 (blue), mitochondria (Tom20, red) and Drp1 (green) in mock treated and Sept2 depleted cells. Scale bar: 10 µm, insets are enlarged fourfold. (B) Quantification of mitochondria-associated Drp1 in mock treated and Sept2 depleted cells (mean of 3 independent experiments, n=44-51 cells) (C) Average distance between mitochondria-associated Drp1 oligomers (representative experiment with n>25 individual mitochondria). (D) HeLa cytosol and crude mitochondrial fractions prepared from mock and Sept2 siRNA treated cells. The samples were analysed by western blotting with indicated antibodies, and show a decrease in mitochondria-associated Drp1 in Sept2 depleted cells.
Simulation of the PFK rate with varying ADP/(ATP+ADP) ratios.Figure 4Simulation 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.
Figure 5Mice were injected in the plantar surface of the hind paw with sumatriptan, or vehicle ± the combination of wortmannin and U0126, as described in the methods section. Mechanical sensitivity was assessed 30 min later using von Frey filaments in an ascending order. (A-C) Percentage of withdrawal response for female mice using von Frey filaments at: 0.07 g (A), 0.16 g (B) and 0.4 g (C). (n= 11-16 per group, ***P<0.001, ****P<0.0001, One way- ANOVA with Tukey's multiple comparison test). Data are shown as mean ± SEM and scatter plots. Mice were injected in the plantar surface of the hind paw with sumatriptan, or vehicle ± the combination of wortmannin and U0126, as described in the methods section. Mechanical sensitivity was assessed 30 min later using von Frey filaments in an ascending order. (D-F) Percentage of withdrawal response for male mice using von Frey filaments at: 0.07 g (D), 0.16 g (E) and 0.4 g (F). (n= 12-16 per group, ***P<0.001, ****P<0.0001, One way- ANOVA with Tukey's multiple comparison test). Data are shown as mean ± SEM and scatter plots.
dTor affects the fat body lipidome via Nep1r1, Ctdnep1 and Lipin A) dTorKO larvae expressing UAS RNAi transgenes or expressing a wild-type dTor cDNA (positive control).Figure 3dTorKO larvae expressing UAS RNAi transgenes or expressing a wild-type dTor cDNA (positive control). The fat body is pseudo-colored red. Topology of NEP1R1, CTDNEP1, and Lipin. Fat body cells labeled by BODIPY to detect neutral lipids. The relative abundance of each lipid class (mean ± SEM) within the set of six membrane lipids. n = 3 MS analyses of 4DO fat body samples for each genotype. ‡ symbols indicate a significant difference compared to w- expressing Luciferase RNAi, * symbols indicate a significant difference compared to dTorKO expressing luciferase RNAi. Note we only tested the effect of Lipin, Ctdnep1, and Nep1r1 RNAi when a lipid class significantly differed between w- and dTorKO. One-way ANOVA, Tukey's multiple comparisons test. * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001 and ‡‡‡‡ p < 0.0001. As above except that TAG abundance was calculated relative to protein. One-way ANOVA, Tukey's multiple comparisons test. Bars show the fraction (mean ± SEM) of membrane GL and GPL lipids with each fatty acyl chain characteristic. n = 3 MS analyses of 4DO fat body samples for each genotype. MUFA, mono-unsaturated; PUFA, poly-unsaturated. ‡ indicate a significant difference between w- and dTorKO expressing Luciferase RNAi, * indicate a significant difference compared to dTorKO expressing Luciferase RNAi. Two-way ANOVA, Dunnett's multiple comparison test. ‡ p < 0.05 and * p < 0.05.
Figure 2A Chitin-induced callose deposition in the mapkkk5 mutants. Seedlings were analyzed at 18 hours after treatment with 10 μM chitin. Representative pictures from the biological replicates are presented. Data are means ±SD from three independent biological replicates, where each biological replicate consists of two technical replicates. The asterisks indicate statistically significant differences from the WT controls by Student's t-test (P < 0.05). B Leaf discs were treated with 10 μM (GlcNAc)7 in a solution containing 500 μM L-012 and 10 μg/ml horseradish peroxidase. ROS production was quantified using a luminescence microplate reader. Data are means ±SD calculated using three biological replicates, where each biological replicate consisted of two technical replicates. C mapkkk5 mutations reduce resistance to Alternaria brassiciicola. Lesions sizes were measured 6 days after inoculation. Values are mean ±S.E., n ≥92. Asterisks indicate significant difference from wild-type controls by Student's t-test (P < 0.01). D Analysis of chitin-induced transcriptional reprogramming in mapkkk5-1. Total RNA was extracted from seedlings treated with mock or 40 μM chitin for 3 hours and analyzed by RNA-seq. Genes that are significantly induced or suppressed by chitin in the wild type were selected (q-value < 0.05; 12,992 genes). The log2 fold changes of the selected genes compared to mock in the wild type and mapkkk5-1 were plotted. Yellow and blue dots indicate genes that show reduced induction or suppression (506 genes) or enhanced induction or suppression (151 genes) in mapkkk5-1 compared to the wildtype, respectively. The slope of the linear regression line (red) indicates that the overall transcriptional response is weakened in mapkkk5-1 compared to the wild type. As a comparison, the line y=x (black) is shown. For more details, see the Methods.E A heatmap showing MAPKKK5-dependent genes. Genes showing reduced induction or suppression in mapkkk5-1 compared to the wild type were selected as described in the Methods (339 genes). The log2 fold changes of the selected genes compared to mock were subjected to hierarchical clustering analysis. Yellow indicates positive values, blue indicates negative values and black indicates zero: see the color scale. F Expression patterns of representative MAPKKK5-dependent genes. qRT-PCR analysis of defense-related genes in 8-day-old seedlings exposed to 40μM (GlcNAc)7 for 3h. Data are shown as the average of three independent biological replicates ± SD. The asterisks indicate statistically significant differences from the WT controls by Student's t-test (P < 0.05).
Figure 9A. Representative Per2::Luciferase traces of Cry1,2-/- SCN slices at baseline (black, arrhythmic), after Cry1 complementation in Prok2+ cells (red) and further complementation in ProkR2+ cells (yellow, rhythmic) (cohort n=8).C. SCN period after Cry1 expression in both Prok2+ and ProkR2+ cells did not differ with order of transduction (p=0.4). D. Bioluminescence rhythm amplitude did not differ with order of complementation (p=0.96). E. Paired goodness-of-fit values for Per2::Luciferase oscillations of baseline, single-transfection and double-transfection SCN (p=0.02, Prok2.Cre before and after, ns. p=0.17; ProkR2.Cre before and after, ns. p=0.99; both Prok2.Cre and ProkR2.Cre applied before and after ****p<0.0001). F. Binary representation of initiated slice elements of a representative SCN slice (CCD recorded bioluminescence pixels) - black indicates non-initiated and pink indicates initiated, i.e., rhythmic elements (cohort n=12). G. Phase map of Per2::Luciferase bioluminescence in a representative Prok2+/ProkR2+ Cry1-initiated SCN slice showing spatial phase synchronisation across the slices (phases colour-coded relative to the mean phase of each slice). H. Inferred neuronal group interactions in relation to circuit-level contribution as "Distributor" or "Integrator" hubs.
Metaphase targeting mutants of M18BP1-1 inhibit nuclear localization during interphase A) Representative images showing G1 localization of human M18BP1WT or human M18BP1SANTA in sfGFP-AID-M18BP1 DLD1 cells treated with 1 mM IAA for 24 h to remove endogenous M18BP1.Figure 7A) Representative images showing G1 localization of human M18BP1WT or human M18BP1SANTA in sfGFP-AID-M18BP1 DLD1 cells treated with 1 mM IAA for 24 h to remove endogenous M18BP1. Centromeric localization is indicated by localization with ACA (α-centromere autoantibody serum), early G1 cell cycle state is indicated by midbody staining in the tubulin channel. M18BP1 species indicated at left, immunolocalized protein indicated above. Scale bar, 10 μm. Insets are magnified 3X. B) Representative immunofluorescence images showing localization of full-length Flag-M18BP1-1 (mutant species indicated at left) without (left panels) and with (right panels) fusion to an SV40 NLS to sperm centromeres in interphase extract depleted of endogenous M18BP1. Immunolocalized protein indicated above. Scale bar, 10 μm. Insets are magnified 3X. Quantification of immunofluorescence intensity at centromeres as total integrated fluorescence signal normalized to wild type levels. The values shown on each panel are represented as a percentage of wild-type Flag-M18BP1-1 ± SEM from three independent experiments. C) Quantification of Myc-CENP-A assembly in M18BP1-depleted extract complemented with the indicated M18BP1-1 species. Graph shows mean immunofluorescence intensity at centromeres normalized to reactions complemented with WT M18BP1-1. Error bars show SEM of at least three independent experiments. D) Representative Western blot of CENP-A assembly reactions in (B). Efficient M18BP1 depletion is indicated by comparing lanes 1 and 10. Add-back of wild-type or mutant M18BP1-1 is near endogenous levels. E) Model showing that metaphase localization of M18BP1 (green) promotes M18BP1 retention on chromosomes during nuclear envelope formation to promote centromeric localization during interphase.