EMBO/sd-character-level-ner huggingface dataset:
Differences in HDX behavior detected upon nucleotide and/or membrane binding.Figure 2(A) Changes in solvent exchange superimposed onto the structure (PDB ID: 2SNH) of the G domain or (B) the stalk/PHD of dynamin in the GMPPCP or lipid bound states, respectively. Key structural elements are identified and the color-coding shows the magnitude of solvent exchange relative to the apo state (see scale below). (C) Differential kinetics of solvent exchange of selected peptides that were identified as altered in both GMPPCP and GDP•AlF4--bound states. The peptides are mapped to secondary structure elements on the polypeptide sequence. Differences in kinetics of solvent exchange of select peptides measured (D) for dynamin bound to GMPPCP in the presence or absence of lipid nanotubes (E) for dynamin bound to lipid nanotubes in the presence or absence of GMPPCP. HDX data are presented as an average of three independent triplicates and color coded as in Figure 1.
Figure 1A Left, time lapse confocal images of PHcrac (red) and LimE (green) in waves at the basal surface of a giant cell. Right, intensity plot across the blue dotted arrow in image "30 sec". Various biosensors in excitable waves. snapshots of biosensors (top) and intensity plots (bottom) across the blue dotted arrows, with black plots showing the corresponding biosensors in images above, red (B) showing PHcrac in the same cell, Scatter plots of biosensor peak locations relative to the peak of PHcrac (C) across propagating waves (blue solid lines indicate median). Positive values indicate that the peak precedes that of PHcrac along the direction of wave propagation. n=26, 26, 24, 21, 21, 32 cells for RalGDS, RBD, PKBA, , respectively. Scale bars in images above represent 20 μm. Grey arrows in all plots represent the direction of wave propagation. Various biosensors in excitable waves. D, snapshots of biosensors (top) and intensity plots (bottom) across the blue dotted arrows, with black plots showing the corresponding biosensors in images above, green (D) showing LimE. E, Scatter plots of biosensor peak locations relative to the peak of or the first peak of LimE (E) across propagating waves (blue solid lines indicate median). Positive values indicate that the peak precedes that of LimE) along the direction of wave propagation. n=26, 26, 24, 21, 21, 32 cells for , RacGEF1, PAK1-GBD, and Coronin, respectively. Scale bars in images above represent 20 μm. Grey arrows in all plots represent the direction of wave propagation. F Left, confocal images of PHcrac (red) and PAK1-GBD (green) in the same cells treated with LatA. Scale bars represent 10 μm. Right, temporal profiles of normalized mean cytosolic intensities of PHcrac (red) and PAK1-GBD (green) (mean±s.e.m., n=18 cells) in response to cAMP. G Cartoon illustrating components and their intensity profiles during wave propagation.
Tumor heterogeneity amongst the major breast cancer subtypes.Figure 6A-C t-SNE plots of combined scRNA-seq profiles of total cells from 8 TNBC tumors, 6 HER2+ tumors and 13 ER+ tumors respectively. Integration and cluster sizes for the same cells Cells colored by cluster (top left panels), EPCAM expression (top right), cancer subtype marker (bottom left) or MKI67 expression (bottom right). Dotted lines delineate epithelial cells (top panels) and cycling epithelial cells (bottom panels). Normal epithelial subsets (normal) are also demarcated by dotted lines in the upper-right panels of B and C. D InferCNV plots to map inferred copy number variation (CNV) for the combined tumor scRNA-seq expression data for the epithelial clusters indicated in panels A-C. scRNA-seq data from normal breast epithelial cells (N-1105-epi) served as a reference for normalization. Each row represents a gene and each column cells from a cluster in a single tumor. The tumor clusters are color-coded as in A-C. Amplifications (red) and deletions (blue) are inferred from the gene expression. Tumor cells were distinguished from normal (N) cells by abundance of CNV. E t-SNE plot of EPCAM+ epithelial cells from ER+ tumors (C). Top panel shows reclustering (resolution 0.05), bottom panel shows expression of MKI67. F Heatmap of cells from clusters in (E) using genes from the PAM50 cancer subtype classifier. G Enrichment of KEGG pathways in EPCAM+ clusters 1 to 3 in (E) for ER+ tumors (Fisher's exact test). H Combined t-SNE transcriptome profiles of two distinct ER+ tumors isolated from the same breast of a patient: ER-0029-7C (blue) and ER-0029-9C (yellow). The corresponding t-SNE cell clusters are shown in the middle panel and expression of EPCAM is shown in the right-hand panel.
Figure 3A Diagram showing BDA-labeled corticospinal axons at certain distances from the spinal lesion border after SCI. BDA (red) was applied into sensorimotor cortex to anterogradely label corticospinal axons. GFAP (blue) was used to label reactive astrocytes and outline the lesion border in the injured spinal cord. The red dashed lines indicate the rostral and caudal borders of the lesion; the green dashed lines indicate various distances from the rostral lesion border (0 mm); the blue dashed lines indicate various distances from the caudal lesion border (0 mm). B-K Representative images of serial sagittal sections showing the main BDA-labeled corticospinal axons in NB-3+/+ (B-D) and NB-3−/− (E-G) mice 14 weeks after complete spinal transection. (H-J) High-magnification images of the areas in (E-G) (single asterisks), respectively. (K) High-magnification image of the area in (E) (double asterisk). The arrows indicate the lesion sites; the white dashed lines indicate the regenerative corticospinal axons extending into the distal spinal cord; the single asterisks in (E-G) indicate the lesion epicenters; the double asterisk in (E) indicates the axons extending from the caudal lesion border. Scale bars, 400 µm (B-G) and 100 µm (H-K).L Quantification of the intensity index of BDA-labeled axons at certain distances from the lesion border in (B-G). Data are represented as mean ± SEM. *p < 0.05, and **p < 0.01; two-way ANOVA followed by Fisher's LSD. n= 25 mice per group.
Figure 1U2OS cells were transfected, synchronized at the G1/S-border by thymidine for 24 hours and then either released into nocodazole for 16 hours (unperturbed mitotic entry) or released for 7 hours, treated with 0.5 μM Adriamycin for one hour and after 16 hour G2 arrest were induced to recover by addition of caffeine (checkpoint recovery). Mitotic index was scored based on the percentage of Histone H3-pS10 positive DAPI-nuclei and normalized to the untransfected controls. Black diamonds indicate individual siRNA-targeted genes from the library, light grey diamonds indicate positive (Wip1-depleted) and negative (untransfected and GAPDH-depleted) controls and dark grey diamonds indicate the hits based on the two screens. Dotted lines indicate selection criteria for recovery-specific genes.
Figure 1(A) General strategy for bacterial CRISPRa using a dCas9 fused with a transcriptional activator, a targeting gRNA, and reporter genes. (B) System components are constructed in three compatible plasmids. CasTA candidates could be cross validated through GFP and antibiotic resistance gene reporters. (C) Fold induction of the fluorescence of CasTA candidates using different gRNAs targeting to different locations of the GFP reporter gene compared to a strain without CasTA. The dCas9-ω was verified in the ∆rpoZ strain background, and the rest of candidates were verified in the wild-type strain (BW25113). (D) Survival of cells containing upregulated antibiotic resistance reporter induced by dCas9 or dCas9-AsiA with gRNA-H3 under kanamycin selection (2.5 μg/ml). (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. (F) Comparing single and multiple gRNA with dCas9-AsiA.
Structure of noisiness shows partitioning between day and night A.Figure 2A. Number of genes identified as being highly variable for each time-point. These genes are separated between those that are also selected as highly variable in at least one other time-point (dark blue) and those highly variable in only one time-point (light blue). The top bar indicates time-points harvested during the day (orange), just before dusk (red), during the night (black) and just before dawn (blue). B. Distribution of the number of time-points at which genes are identified as highly variable (blue) or lowly variable (green). The distribution of average (black) and 95% confidence interval (dotted grey) for the thousand random sets is also represented. C. Heatmap of the percentage of HVGs shared between time-points. Red indicates a high percentage of HVGs in common between two time-points. The top and side bars indicates time-points harvested during the day (orange), just before dusk (red), during the night (black) and just before dawn (blue). D. Hierarchical clustering of HVGs based on the log2(CV2/trend) at each time point. The result is represented as a heatmap where yellow indicates a high log2(CV2/trend). The genes were separated into four clusters, indicated by the side colored bar. The top bar indicates time-points harvested during the day (orange), just before dusk (red), during the night (black) and just before dawn (blue). See Appendix Fig S3G for heatmaps of the log2(CV2/trend) with the same colour cutoffs for HVGs, LVGs and random genes. E. Heatmap of the mean normalised expression level for the genes in Fig 2D, keeping the same clustering organisation. The top bar indicates time-points harvested during the day (orange), just before dusk (red), during the night (black) and just before dawn (blue).
DIA1(R1204X) induces elongation of microvilli in MDCKmCherry-ESPIN1 cells.Figure 2GFP-tagged DIA1, DIA1(M1190D), and DIA1(R1204X) plasmids were transfected into MDCKmCherry-ESPIN1 cells cultured on membrane inserts. Twenty-four hours after transfection, a reconstructed lateral view of fixed cells was generated using a confocal laser fluorescence microscope. Arrows indicate the elongated microvilli visualized by mCherry-ESPIN1 with GFP-hDIA1(R1204X) expression. Scale bars: 5 μm. Representative of 3 experiments.
Figure 4A Mapping results for segregant pools involving the indicated TS alleles and wild strains. The change in S288C allele frequency between the meiotic progeny isolated at 26°C and 34°C is plotted by genomic coordinate. Causal suppressor genes are indicated for regions that show selection for the wild strain sequence. Genes in brackets have not been validated experimentally. B B Comparison of the change in reference allele frequency, either for suppressor loci for which a causal suppressor gene was validated (N=17), or for loci for which we were unable to validate a suppressor gene (N=10). Loci for which all experiments failed due to technical reasons were excluded from the analysis. Statistical significance was determined using a two-tailed Mann-Whitney's U test (** = p < 0.005). Boxes: first, second, and third quartiles; whiskers: 1.5 interquartile range away from the first and third quartiles. C A cartoon of the TORC2 signalling pathway, highlighting suppression of a TORC2 mutant (tsc11) by mutations in ORM2. D D Suppressor prediction within the chromosome XV QTL of rpn11 TS mutants. The functional information prioritisation score (y-axis) for genes in the suppressor region (x-axis) identified RPT4 and RPN8 as the two highest-scoring suppressor candidates. E E Experimental validation of RPN8 as the causal suppressor of the rpn11-8 TS mutant. Cultures of the indicated strains were diluted to an optical density at 600 nm of 0.1 and a series of ten-fold dilutions was spotted on agar plates and incubated for 2-3 days at 34°C. UWOPS = UWOPS87-2421. See also Figure EV4.
Fig.Figure 1A: Schematic domain composition of PBANKA_1317200, showing predicted ER signal peptide (red), apicoplast transit peptide (green), transmembrane helices (dark grey), NADP(H) binding (pink) and NAD(H) binding (blue) modules. Functional NTH domains I, II and III are indicated. B: Predicted functions of the P. berghei NTH protomer in the lipid bilayer showing functional domains I-III and corresponding functional activities. C: Organisation of functional NTH domains I-III (coloured bars) in T. thermophilis, E. coli, mammals, and Plasmodium. Linker connecting functional domains is indicated by dotted line. Prokaryotic nth genes are segmented into three (T. thermophilis) or two (E. coli) segments, encoding NTH subunits α1, α2 and β (T. thermophilis) or α and β (E. coli). Eukaryotic nth genes are unsegmented and encode single polypeptide NTH of different orientations, either corresponding to an αβ linkage (mammal), or to a βα linkage (Plasmodium). The amino (N) and carboxy (C) termini of the eukaryotic NTH polypeptides are indicated.
Figure 3(A) Expression levels of genes involved in steroidogenesis normalized to WT. The bar graphs show means ± SEM (data derived from RNA-seq analysis of testes, biological replicates, n = 5, one-way ANOVA with Tukey's multiple comparisons test, *P < 0.05, **P < 0.01, ***P < 0.001, ns = not significant). (B) Serum levels of A-dione in WT males, ARLmon/Y and AR-/Y mice at the age of 13 weeks. (C) Expression levels of Hsd17b3 normalized to WT. The bar graphs show means ± SEM (data derived from RNA-seq analysis of testes, biological replicates, n = 5, one-way ANOVA with Tukey's multiple comparisons test, **P < 0.01, ***P < 0.001). (D) Reporter gene assays in Hela cells co-transfected with the mouse Insl3 promotor together with the WT or mutant mouse AR. (E) Schematic overview of the feedback mechanism between testes and pituitary in the transcriptional regulation of steroidogenic genes.
RsaI responds to glucose through the transcriptional factor CcpA.Figure 1(A) Northern blot experiments show the expression of RsaI during growth phase in the HG001 strain in MHB medium with or without the addition of 1,5 g/L of D-glucose. Glucose was added either at the beginning of growth (+ glucose, left panel) or after 3h of growth (right panel). (B) Northern blot experiment shows the expression of RsaI during growth phase in the HG001, ∆ccpA mutant strain, and ∆codY mutant strain, in MHB medium with (+) or without (-) the addition of 1,5 g/L of D-glucose. (C) Northern blot experiment shows the expression of RsaI in the HG001 and ∆ccpA mutant strains. Total RNA was prepared after 2, 3, 4, 5 and 6h of culture in BHI medium at 37°C. (D) Northern blot analysis of RsaI in the HG001 strain grown in MHB medium with or without the addition of 1 g/L of glucose, fructose or xylose. For all the experiments, loading controls were done using the expression of 5S rRNA (5S) as revealed after hybridization of the membranes with a specific probe. However for these controls, we used aliquots of the same RNA preparations but the migration of the samples was performed in parallel to the experiments on a separate agarose gel because RsaI and 5S rRNA have very similar sizes.
Figure 2B) Characterization of the Doxycycline-inducible cell lines expressing siRNA resistant wild type (WT) or mutant (TMA or TMD) FLAG/HA-tagged PALB2. The cell lines were transfected with UNC (Negative Control) or PALB2 siRNA for 24 hours prior to induction with Doxycycline. Immunoblots were performed with indicated antibodies. C) Cell line characterization of FLAG/HA-tagged PALB2 localization 2 hours following exposure to 15 Gy of IR. Z-stack max intensity image projection and background subtraction was done using ImageJ/Fiji. Scale bar = 5μm. D) Kinase assay was performed as described in Figure 1E except that the SDS-PAGE gel was Coomassie stained following electrophoresis. WT was used at two different concentrations (1x and 0.75x). E) Doxycycline-inducible stable U2OS cell lines were left untreated or treated with Doxycycline and/or IR (15 Gy, 2h recovery). Following protein extraction the lysates were immunoprecipitated (IP) with IgG or antibody recognizing phosphorylated S/Q sites (pS/Q) and analyzed by SDS-PAGE. Immunoblots were performed with indicated antibodies.
Figure 1Schematic representation of neuron remodeling of γ-KCs and its regulation by the nuclear receptors EcR and UNF. p: axon peduncle; m/v: medial and vertical lobes. Dynamic expression of Dprs and DIPs during γ-KCs development. Left: Heatmap depicting the relative expression patterns of Dprs and DIPs in γ-KCs during development. Middle: Magenta intensity depicts the peak expression of each gene during development relative to other Dprs and DIPs. Right: Expression change of Dprs and DIPs while knocking down the UNF transcription factor compared to WT γ-KCs. Dprs highlighted in bold were tested in the RNAi mini-screen (Figure EV1). Confocal z-projections of the indicated genotypes and age, labeled with membrane bound GFP (mCD8-GFP; CD8) driven by the γ-specific Gal4 driver GMR71G10-Gal4 (γ-Gal4). While γ-axons of control flies project through the entire lobe (C is the RNAi control; n=12/12, E; is the tsCRISPR control; n=14/14), knockdown of dpr12 by RNAi (D; n=12/12) or knockout by tsCRISPR (F; n=14/14) resulted in short axons. At L3, γ-axons in dpr12∆50-81 homozygotus mutant animals (K; n=20/20) resemble WT γ-axons (G; n=20/20). At 48hr APF, γ-axons normally re-extend to form the adult lobe (H; n=12/12). dpr12∆50-81 γ-axons (L; n=14/14) fail to extend to the end of the lobe. This defect persists to adult (I; n=11/11 vs. M; n=18/18). Expressing a UAS-Dpr12 transgene within γ-KCs in dpr12∆50-81 homozygote mutant animals rescued the axon regrowth defect (N; n=23/24, J; n=14/14). The adult γ-lobe and α/β lobes are outlined in (C, D) in yellow and orange, respectively, for clarity. Asterisks demarcate the distal part of the lobe. Green and white indicate mCD8-GFP. Magenta represents FasII staining. Scale bar is 20 µm. Quantification of the regrowth defects in I, M and N. The z-projections were blindly classified into four classes of regrowth defect severity, see Figure EV1D for examples. Significance was calculated by Kruskal-Wallis test followed by a Mann-Whitney post-hoc test; ***p<0.001. Models based on hemibrain EM-traces (Scheffer et al., 2020) of adult γ-KCs (representative neurons shown in green), in relation to either selected PAM-DANs (left; red and orange) or MBONs (right; cyan and blue) targeting the γ4 and γ5 zones. Note that the cell body of the γ4-MBON is located in the contralateral hemisphere. The MB neuropil is shown in grey. See methods for additional details. Schematic representation of the adult MB. The bundled γ-KCs form the γ-lobe (an example of a single γ-KC is depicted in green). The γ1-γ5 zones are defined by stereotyped and tiled innervations of the γ-lobe by dopaminergic neurons (DANs; examples of DANs targeting the γ4 and γ5 zones are depicted in red and orange, respectively) and MB output neurons (MBONs; an example of the γ4>γ1γ2 MBON innervation is shown in cyan to match the schematics in Figure 7E-F; note that its cell body and innervations are located in contralateral hemispheres). Black dashed line represents the midline. Magenta represents typical FasII staining (which stains the α/β lobes and the γ-lobe but not the α'/β' lobes).
Genome-wide localization of HERVs relative to promoters and enhancers (A) Comparison of regions annotated "LTR" in RepeatMasker with the regions annotated TssA, TssAFlnk, Enh, EnhG, TssBiv, or EnhBiv in the 15 core marks model of the Epigenomic Roadmap consortium (referred to as PEs for Promoters and Enhancers).Figure 1Comparison of regions annotated "LTR" in RepeatMasker with the regions annotated TssA, TssAFlnk, Enh, EnhG, TssBiv, or EnhBiv in the 15 core marks model of the Epigenomic Roadmap consortium (referred to as PEs for Promoters and Enhancers). For each tissue, the Jaccard index comparing PEs to LTRs is divided by the average Jaccard index (1000 iterations) obtained when comparing PEs to randomly selected genomic locations (of the same sizes as the LTRs). Only the 10 tissues with the highest and the lowest score are shown. Full list in Appendix Figure S1A. Profile reporting the position of regions annotated "LTR" in RepeatMasker relative to PEs from the indicated tissues. Red and blue horizontal lines materialize the level of LTR density expected in a random sequence from pancreatic islets and human embryonic stem cell line HUES6, respectively. A graphic interpretation of the positioning of PEs at the bottom of LTR-valleys in panel (A). Example of a region annotated "LTR" in RepeatMasker and overlapping with a PE and with a CAGE peak from the FANTOM5 consortium data, indicative of a site of transcription initiation. Biological process GO terms associated with genes located 100 kb or less from a region annotated "LTR" in RepeatMasker and overlapping with a PE and with a CAGE peak.
PTB RRM2 interacts with multiple RNA‐binding proteinsSchematic representation of PTB (top) and the GST‐PTB RRM2 (below), with the limits of the PTB minimal repressor domain indicated.Figure 1A Schematic representation of PTB (top) and the GST‐PTB RRM2 (below), with the limits of the PTB minimal repressor domain indicated. PTB is composed of four RNA recognition motifs (RRM) with three linker regions in between them. It also contains a N‐terminus bipartite nuclear localization signal (NLS) as well as a nuclear export signal (NES). The GST‐PTB RRM2 is composed of the second RRM fused to a GSTtag in the N‐terminus. B Silver stain of the GST‐PTB RRM2pull‐down of the wild‐type RRM2 and the Y247Q mutant. Five microlitre of the pull‐down was run on a 15% SDS-PAGE and silver‐stained. Three strong bands can be seen which are due to the recombinant protein and the beads used for the pull‐down. The region encompassing 50 kDa to the top of the gel was sliced and subjected to in‐gel digestion and mass spectrometry. The two strongest bands visible in this region are labelled as Matrin3 and Raver1. C Proteins identified in the GST‐PTB RRM2 pull‐down ranked by their unique peptide number. The table shows the different proteins we found binding to RRM2, as well as when present, the sequence of the PRI motif. The indicated function is only a guideline as many have more functions than shown. D Western blot of the GSTpull‐down using antibodies against Matrin3 and Raver1. Lanes 1 and 2 show 5 and 10% of input, respectively, lanes 3 and 4 show GST‐PTB full‐length pull‐down of wild‐type and Y247Q mutant, respectively, and lanes 5 and 6 show GST‐PTB RRM2 pull‐down of wild‐type and Y247Q mutant, respectively, and lane 7 with pull‐down using GST alone.