EMBO/sd-character-level-ner huggingface dataset:
Oscillation in metabolite concentrations throughout the cell cycle in HeLa cells.Figure 2Figure 2: Oscillation in metabolite concentrations throughout the cell cycle in HeLa cells. The figure shows metabolites found to significantly oscillate throughout the cell cycle (concentrations normalized per metabolite; maximal concentration in red; minimal concentration in blue). The amplitude of the oscillations is shown on the right. Metabolites are color-coded according to metabolic pathways: Energy/redox cofactors (purple); amino acids (blue); glycolytic metabolites (red); TCA cycle metabolites (green).
Modelling the circadian regulation of CDF1 and FKF1 mRNA.Figure 2Schematic of proposed circadian regulators of FKF1 and CDF1 transcription. Experimental validation for CCA1 regulation of the flowering pathway. ChIP data showing CCA1 enrichment in regions containing CCA1 elements (CBS or EE; white bars) in GI, FKF1 and CDF1 promoters, compared to regions of their respective exons (dark bars). Locations of primers for GI (GI-a, GI-N), FKF1 (FKF1-a, FKF1-N) and CDF1 (CDF1-a, CDF1-N) are shown in Supplementary Fig S3. Seedlings were grown for 14 days 12L:12D cycles at 22°C and harvested at ZT2. Statistical analysis performed using Welch tests, *P < 0.005. Error bars represent standard error of technical replicates. CDF1 mRNA in LDs (C) and FKF1 mRNA in SDs (D), from WT (data: black lines, filled squares; simulation: black lines), and the cca1;lhy mutant (data: green lines, open circles; simulation: dashed green lines) (data sets used for parameter optimisation). CDF1 (E) and FKF1 (F) mRNA data in LDs, from WT (as in C, D) and the prr9;7 mutant (blue-green line, open circles). CDF1 (G) and FKF1 (H) mRNA simulations in LDs, from WT (as in C, D) and the prr9;7 mutant (dashed blue-green line).
Figure 5AFraction (left) and speed (right) of motile hemolymph sporozoites on glass . Dots correspond to individual experiments and bars indicate the mean. Box‐and‐whisker plots depict the 25% quantile, median, 75% quantile, and nearest observations within 1.5 times the interquartile range (whiskers). Significance for (A left) and (B left) determined by One-way analysis of variance with Tukeys Multiple Comparison test. Significance for (A right) and (B right) determined by Kruskal-Wallis test with Bonferroni's Multiple Comparison test. C. Selected trajectories of 20 manually tracked sporozoites isolated from hemolymph and moving over a period of 3 min. Scale bar, 10 μm. D. Selected trajectories of 20 manually tracked sporozoites isolated from salivary glands and moving over a period of 3 min. Scale bar, 10 μm.
Figure 5(A) % CpG methylation of 20 kb tiles in 5% bins in control or Tet-TKD 2-cell embryos. All samples from one condition were merged for this visualization. (B) % CpG methylation of 500 bp tiles for different genomic features. All samples from one condition were merged for this visualization. Intergenic = genome excluding gene bodies and TSS -5 kb/+1 kb; Gene bodies = genes excluding TSS -5 kb/+1 kb; Promotor-CGI = CGIs overlapping TSS -5 kb/+1 kb; Non-CGI promoter = promoter (TSS -5 kb/+1 kb) not close to CGI; Non-promoter CGI = CGIs not overlapping TSS -5 kb/+1 kb. (p-values were calculated using a Wilcoxon matched-pairs signed rank test and presented in a medium smoothed violin plot with indicated median and quartiles as dotted lines, **** = p < 0.0001; mean difference is indicated above the plot). (C) Heatmap of differentially methylated uniquely mapped 500 bp tiles. Shown are random 20% of all significantly hypo- (450 of 2253) and hyper-methylated (2063 of 10316) tiles (logistic regression function of Seqmonk, padj< 0.01, difference 20%, for details see method section). (D) Distribution of differentially methylated tiles over promoter, gene bodies, or intergenic sequences. (E) Correlation of significant DNA methylation changes in promoter regions and differentially expressed genes. Numbers in boxes represent number of genes. (F) Significant methylation changes of specific TEs subdivided in different classes of TEs (calculated using logistic regression function of Seqmonk, padj < 0.05; data are represented as medium smoothed violin plot with indicated median and quartiles as dotted line). (G) Correlation of significant DNA methylation changes in TEs (calculated with logistic regression function of Seqmonk, padj < 0.05, methylation difference >5%), which are also significant differentially expressed (DEseq2, padj < 0.05, |log2FC|>0.7). (H) Developmental rate of embryos derived from control, Tet2-MO2, Tet2-MO2 + Tet2 full-length mRNA (as shown in Fig. 1E) and Tet2-MO2 + Tet2 truncated mRNA (no catalytical domain) injected oocytes. Indicated p-values were calculated using the log rank (Mantel-Cox) test against Tet2-MO2 KD or as indicated (* = p < 0.05, *** = p < 0.001, **** = p < 0.0001, numbers of analyzed embryos for each condition is indicated in parenthesis).
Depletion of the expression of members of the seven gene set reduces CRPC cell proliferation and AR ligand-independent transcriptional activity.Figure 3Cell proliferation was examined in the CRPC cell line 22Rv1 following individual depletion of mRNAs for the seven genes or shGFP controls, using shRNA against the coding region for each gene (shRNA #2). Cell number was measured using a non-perturbing nuclear restricted dye and quantified after 72 hours using Incucyte Zoom System. Data shown are mean ± s.e.m. of 8 to 12 replicates normalized to their shGFP control. Kruskal-Wallis test (p value < 0.0001, two-tailed) and Dunn's multiple comparisons test were performed. Representative images of 22Rv1 stably depleted of BUB1B, or control (shGFP) are shown. 22Rv1 stably depleted of each of the seven genes were transfected with a dual plasmid luciferase reporter system which quantifies AR activity and basal transcription. The assay was conducted in 2% CSS to measure AR ligand-independent transcriptional activity. Data represent two independent experiments performed in triplicate, showing the mean ± s.e.m., and normalized to their shGFP controls. Kruskal-Wallis test (p value < 0.0001, two-tailed) and Dunn's multiple comparisons test were performed. * Significant at a p value < 0.05, ** p value < 0.001. The expression of FKBP5 and UBE2C determined by RT-qPCR analysis and normalized to GAPDH mRNA levels was examined in 22Rv1 cells stably expressing shRNA for each of the seven genes. Cells were cultured in 2% CSS. Data represent two independent experiments performed in duplicate or triplicate, showing the mean ± s.e.m., and normalized to their shGFP controls. Kruskal-Wallis test (p value < 0.0001, two-tailed) and Dunn's multiple comparisons test were performed. * Significant at a p value < 0.05, ** p value < 0.001.
Figure 3Real-time RT-PCR analysis of mRNA levels of ER-GATA-1 target genes in untreated or b-estradiol-treated (48 hours) WT and mutant clones. ***, P < 0.001 with respect to all values of WT1-3 (n = 4, mean +/- SE).
Figure 5 Schematic designs for metabolic energy measurements at different temperatures and after i.p. injection of CL316243 (CL). Changes between 2 temperatures occurred linearly at 2 h  Average energy expenditure of 3.5- to 4.5-mo-old male and female mice measured at 22oC, 30oC and 4oC in Oxymax chambers under a light/dark period for 12, 10 and 4 h, respectively (CP2-KO/WT/Ucp1ΔL/UCP1-KO: n = 5/5/4/4 male mice and 5/6/5/3 female mice). WT mice were pooled from littermates of CP2-KO mice and Ucp1ΔL mice. *p < 0.05, **p < 0.01 compared with WT mice, one-tailed unpaired Student's t test. All groups of mice showed similar mean body weight (CP2-KO/WT/Ucp1ΔL/UCP1-KO: male, 28.6 ± 1.6/33.4 ± 2.0/29.7 ± 2.6/30.4 ± 2.6 g; female, 26.4 ± 1.8/28.0 ± 1.8/27.6 ± 3.0/27.2 ± 3.0 g)  Blunted CL-promoted energy expenditure in CP2-KO, Ucp1ΔL and UCP1-KO mice of both sexes (***p < 0.001 compared with WT mice by two-way ANOVA). Data at the denoted time points are the average of 7 data points acquired before a 126-min period. ap < 0.05 CP2-KO mice, bp < 0.05 Ucp1ΔL mice or cp < 0.05 UCP1-KO mice compared with WT mice by Tukey's post hoc test
Fig.Figure 5(A) Side view of NHE9 monomer constituted by 6-TM core transport domain (blue), dimerization domain (orange) and linker helix TM7 (grey) showing the extracellular hydrophobic gate in the inward-conformation between TM12b (yellow spheres) and TM3 (purple spheres and black boxes in alignment). The hydrophobic barrier is made up of highly conserved residues in TM3 of the dimer domain that face towards the transport domain; indicated as purple spheres. The asterisk (*) indicates hydrophobic residues in TM5b of the transport domain that are likely to form an intracellular hydrophobic gate in the outward-facing state as based on outward NapA. (B) Inward-facing (left) and outward-facing (right) NHE9 model snapshots along a trajectory following the major Principal Component (PC1) derived from analysis of the conserved Na+/H+ antiporter structural alignment (see Materials and Methods). Extracellular and intracellular hydrophobic gates are coloured as in (A). (C) Schematic representation of NHE elevator alternating-access mechanism highlighting the role of negatively charged phosphoinositide lipids to stabilize homodimerization (left) and the hydrophobic gates formed either side of the ion-binding aspartate (right).
Figure 5A) Schematic representation of the p120-MS2bs minigene construct, which contains two MS2-binding sites in its minor intron instead of the hnRNP H binding motifs. B) Western blot confirming the expression of MS2CP fusion proteins. Extracts from mock transfected HeLa cells, FUS-FLAG, and MS2CP fusion protein expressing cells were subjected to SDS-PAGE and western blot followed by detection of exogenous proteins by anti-FLAG (green, lanes 1-2) and anti-MS2 (green, lanes 3-5) antibodies, respectively. Tyrosine tubulin (red) served as loading control. C) The ratio of spliced to unspliced p120-MS2bs RNA was determined by RT-qPCR from cells expressing the indicated MS2 fusion proteins. Average values and standard deviations of seven biological replicates are shown. D) Schematic representation of MS2-FUS deletion constructs used in the tethered splicing assay shown in E) and F). E) Western blot confirming the expression of MS2CP fusion proteins as in B). The MS2 fusion proteins were detected by anti-MS2 antibodies (green) and tyrosine tubulin (red) served as loading control. F) The ratio of spliced to unspliced p120-MS2bs RNA was measured as in C). Average values and standard deviations of at least three biological replicates are shown. G) Schematic representation of the p120-MS2bs-ex7 minigene construct, which contains two MS2-binding sites in exon 7. H) Western blot confirming the expression of MS2CP fusion proteins as in E). I) The ratio of spliced to unspliced p120-MS2bs-ex7 was measured as in C). Average values and standard deviations of three biological replicates are shown.
HXT2 mRNA enrichment in the bud under glucose shift conditions provides a growth advantage to daughter cells.Figure 7A Schematic depiction of the growth assays. Cells expressing only one hexose transporter at a time were picked from a plate, serially diluted and plated on fresh YPD plates. HXT2 only strains grow faster than the other HXT only strain. Growth was assessed 2-3 days after incubation at 30°C. C Workflow for the competition assay presented in (D). O/N cultures of HXT-only strains were diluted to the same OD600 and pooled. A sample was taken ('start'), the rest of the culture incubated O/N at 30°C. Cells were harvested ('end'), DNA was isolated from both samples, and the amount of HXT DNA was determined by qPCR. D Quantification of competition assay. qPCR with primers against either HXT1, 2, 3 or 4 was performed. HXT gene abundance was normalized against actin. E Strains that lack HXT2 grow slower when coming from quiescence compared to WT. F Tagging the HXT2 mRNA with U1A stem loops leads to its artificial enrichment in the bud in 96% of cells independently of the cell cycle. Arrows point to examples of HXT2-U1A mRNA in the bud early and late in the cell cycle. G Cells that always enrich HXT2 mRNA in the bud have a growth advantage in the first hours when coming from quiescence compared to WT or cells that only express HXT2. H Daughter cells do not retain a memory of the previous stress situation encountered by their mothers. Cells were re-fed after starvation and analyzed for enrichment of HXT2 mRNA via FISH at different time points. Proposed model for the regulation of the asymmetric HXT2 mRNA distribution when cells come out of starvation or leave the quiescent state. For details, please see text.
Figure 3A Images of B. subtilis WT and Δbkd cells co-labelled with the membrane potential-sensitive dye DISC3(5) and the membrane permeability indicator Sytox Green. Membrane properties were assessed for Δbkd cells grown in the presence of MB, IB or washed precursor-free (IBPF) for the times indicated. As controls, WT cells were measured in the presence of depolarising antimicrobial peptide gramicidin ABC (gABC) or pore-forming lantibiotic Nisin. For cross-correlation between membrane depolarisation and membrane permeabilisation, see Appendix Fig S3A-C. B Quantification of DISC3(5) fluorescence for cells (n=100-142) depicted in panel A. Median represented by red line. C Images of E. coli WT and fabA(Ts) cells co-labelled with the same indicator dyes as in panel A. Membrane properties were assessed for fabA(Ts) at 30°C and upon transfer to non-permissive 37°C for the times indicated. As controls, WT cells were incubated with the pore-forming antibiotic Polymyxin B (PolyB). For cross-correlation between membrane depolarisation and membrane permeabilisation, see Appendix Fig S3D and E. The integrity of the diffusion barrier function was additionally studied via ONPG permeability in a ΔlacY background (see Fig EV1). D Quantification of DISC3(5) fluorescence for cells (n=76-141) depicted in panel C. Median represented by red line. Dat
Requirement of the LIR motif for the critical role of NBR1 in heat tolerance.Figure 10(A) Diagrams of wild-type and mutant NBR1 proteins. The conserved W and I residues in the LIR motif between the two UBA domains were changed to A residues in the NBR1W661A/I664A (mNBR1) mutant protein. (B) Five weeks-old Arabidopsis Col-0 wild type (WT), nbr1 and transgenic nbr1 plants expressing the wild-type NBR1 (lines 3 and 6; see Figure S2) or the NBR1W661A/I664A (mNBR1) (lines 2 and 6; see Figure S2) mutant gene were placed in a 45°C growth chambers for 10 hours and then moved to room temperature for 3-day recovery before the picture as taken. The experiment was repeated three times with similar results.
Figure 5A. Strategy for identification SPATA2-dependent protein association with the TNF-RSC. SPATA2 was knocked down using RNAi, cells were stimulated with FLAG-TNF-α, and the TNF-RSC was enriched from control and SPATA2 knockdown cells as in Figure 3A. The enriched proteins were quantified using SILAC-based MS. B. Effect of SPATA2 knockdown on association of proteins with TNF-RSC. The list shows SILAC ratios of TNF-RSC-associated proteins in control cells and SPATA2 knockdown cells. The proteins that showed reduced association with the TNF-RSC after SPATA2 knockdown are highlighted red. C. Validation of SPATA2-dependent association of CYLD with the TNF-RSC. The TNF-RSC was purified under the indicated conditions and association of SPATA2, CYLD, RIPK1 and HOIP with the TNF-RSC was analyzed by immunoblotting. The input controls show expression of the analyzed proteins in cell lysates. The asterisk denotes unspecific bands.
expression and binding to TNC(A) Heat map representation of the most 17 deregulated Panther identified immune related genes in TNC high (WT/shC) and TNC low (KO/shTNC) tumors (N = 2 tumors each).Figure 3(A) Heat map representation of the most 17 deregulated Panther identified immune related genes in TNC high (WT/shC) and TNC low (KO/shTNC) tumors (N = 2 tumors each). (B) CXCL12 protein levels in NT193 tumors (ELISA). N = 7 tumors per group, ** p = 0.0035 (WT host, shC versus sh1TNC), ** p = 0.0070 (WT host, shC versus sh2TNC), * p = 0.0379 (TNCKO host, shC versus sh1TNC), * p = 0.0262 (TNCKO host, shC versus sh2TNC), Mann-Whitney test. Mean ± SEM. (C) Cxcl12 levels in cultured tumor cells (qRT-PCR). N = 5 independent experiments, ** p = 0.0079, Mann Whitney test. Mean ± SEM. (D) CXCL12 protein levels (ELISA) in conditioned medium (CM) from cultured tumor cells, N = 6 independent experiments, ** p = 0.0022, Mann Whitney test. Mean ± SEM. (E) Analysis of Cxcl12 (qRT-PCR) in tumor cells upon pretreatment with the indicated inhibitors for 45 minutes (GW, BOP, DMSO and PBS as control respectively) or 60 minutes (Sunitinib) and 6 hours (Cli95) (6 hours DMSO as control) before incubation with TNC for 24 hours. N = 6 independent experiments, ** p = 0.0022, Mann Whitney test. Mean ± SEM. CXCL12 binding to TNC as determined by SPR measurement CXCL12 binding to TNC as determined by negative EM imaging (G), followed by quantification (H). (G) scale bars, 100 nm (left), 50 nm (right), the arrowheads point at gold labeled CXCL12 and the asterisk points at the fibrinogen globe of the murine TNC monomer. (H) Representation of TNC monomer, oligomerization domain (triangle) to form hexamers as seen in (G), FNIII repeats (grey boxes, contant domains, white boxes, alternative domains), fibrinogen like domain (circle). Representative result (3 independent experiments).
Figure 3A. Confocal images of coronal sections from E16 brains of miR-34/449 KO mice and littermate controls (Het), stained with anti-Satb2-antibody to label neurons of layers II-IV (green) and DAPI to label all cell nuclei (blue). Scale bars: 50 μm.B. Quantification of the number of Satb2-positive cells per 100 μm ventricular zone surface. Bars indicate mean ± SEM, as for all quantifications shown in this figure; n = 3 brains per genotype group, from two independent litters. Data was normalized (norm.) to the ventricular zone surface analyzed (100 µm) and relativized to the heterozygous control average value. Significance was tested by Welch's t test: p-value = 0.01146 (Het vs. KO) (n = 4 cortices per genotype group, 2 independent litters). All subfigures were statistically tested as in B. * indicates p ≤ 0.05, ** indicates p ≤ 0.01, *** indicates p ≤ 0.001. C-J. Confocal images and cell density quantifications as in A using molecular markers for different cell types:C, D. E16 brains stained with anti-Ctip2 antibody to label layer Vneurons (n = 4 brains per genotype group, 2 independent litters). Scale bars: 50 μm. Images in C were taken from same brain slices as shown in A. p-value = 0.03224 (Het vs. KO) (immuno co-staining of Ctip2(red, C)). C-J. Confocal images and cell density quantifications as in A using molecular markers for different cell types:E, F. E14 brains stained with anti-Tbr1 antibody to label layer IVneurons p-value = 0.01392 (Het vs. KO) (n = 3 and 4 brains per genotype group from 2 independent litters). Scale bars: 50 μm. C-J. Confocal images and cell density quantifications as in A using molecular markers for different cell types:G, H. E16 brains stained with anti-Tbr2 antibody to label intermediate progenitors. p-value = 0.01647 (Het vs. KO) (n = 7 brains for each genotype group, 5 independent litters). Scale bars: 50 μm. C-J. Confocal images and cell density quantifications as in A using molecular markers for different cell types:I, J. E16 brains stained with anti-Pax6 antibody to label radial glia progenitors. p-value = 0.002768 (n = 5 brains per genotype group, 3 independent litters). Scale bars: 50 μm. K. 3D reconstruction of a dividing radial glial progenitor at early anaphase. A coronal section of an E14 brain of a heterozygous control mouse was stained with anti-phospho-Vimentin antibody (red), anti-γ-tubulin antibody (green/yellow), phalloidin (magenta), and DAPI (blue) and imaged by 3D confocal microscopy. "s" indicates spindle axis, "α" indicates angle relative to ventricular surface plane, which was determined by a vector path as indicated by thin white lines located on the left side of the image. Yellow dots highlight the centrosomes of the spindle poles from the analyzed dividing cell. Scale bars: 5 μm.L. Quantification of spindle orientation in radial glial cells as in K for E14 brains of miR-34/449 KO and littermate controls (Het). Each dot represents a single dividing cell; p-value = 3.166e-05 (Het vs. KO) (n = 131 vs. 107 cells, n = 4 brains per genotype group, 2 independent litters).
AltFUS is necessary for FUS-associated inhibition of autophagy and accumulation of FUS/TDP-43 cytoplasmic aggregates A, Images by confocal microscopy of mCherry-GFP-LC3 signal in HeLa cells across biological conditions: untreated mock, bafilomycin treated mock, altFUS, FUS, FUS(Ø), FUS-R495x and FUS(Ø)-R495x (representative images of n=3).Figure 4A, Images by confocal microscopy of mCherry-GFP-LC3 signal in HeLa cells across biological conditions: untreated mock, bafilomycin treated mock, altFUS, FUS, FUS(Ø), FUS-R495x and FUS(Ø)-R495x (representative images of n=3). The altFUS signal (white) is shown as an inset in the top or bottom left of the left panels. The white scale bar corresponds to 10 μm and the zoomed in region (right panels) is delimited by a white box. B, LC3-II accumulation after bafilomycin treatment from mock, altFUS, FUS, FUS(Ø), FUS-R495x, FUS(Ø)-R495x transfected cells and FUS(Ø)-R495x and altFUS co-transfected cells across 3 independent experiments (n=3, mean ± SD). The quantification corresponds to the treated/untreated ratio of LC3-II abundance Statistical significance is relative to the mock condition unless otherwise indicated (**** = p value < 0.0001, *** = p value < 0.001, ** = p value < 0.01, n.s. = non-significant, two-way ANOVA with Tukey's multiple comparison correction). C, Images by confocal microscopy of altFUS (Flag tagged - white), FUS (GFP tagged - green) and TDP-43 (red) signals in HeLa cells transfected with the bicistronic GFP-FUS(Flag)-R495x or the monocistronic GFP-FUS(Ø-Flag)-R4955x constructs, or co-transfected with the monocistronic GFP-FUS(Ø-Flag)-R495x and altFUS-Flag constructs (representative images from n=3). The white scale bar corresponds to 10 μm. D-E, Quantification of FUS cytoplasmic granules, number (D) and area (μm2) (E) in cells over-expressing the bicistronic (+) or monocistronic (-) construct for FUS, FUS-G156E, FUS-R495x, FUS-K510E, FUS-Q519x, FUS-Q519I-fs527x, FUS-R521C, and FUS-P525L. Statistical comparisons are made between bicistronic and monocistronic versions of each construct (n=3 - biological replicates, mean ± SD, **** = p value < 0.0001, *** = p value < 0.001, ** = p value < 0.01, * = p value < 0.05, n.s. = non-significant, one-way ANOVA test with Sidak's multiple comparison).