EMBO/sd-character-level-ner huggingface dataset:
Figure 1A. Pedigree of the extended family. Filled symbols indicate affected members. Arrow indicates the proband. Circles-females; squares-males; Slant-deceased; asterisk-No DNA available for molecular diagnosis. B. Phenotype of the patients as indicated. (a) Sparse woolly hair. (b) Protrusion of upper lip due to deformity of teeth. (c) Ichthyosis-like fine scale and erythema. C. Images of the heart of the patients as indicated. (a) M-mode echocardiography taken from the parasternal long axis view of the left ventricle (LV) illustrating poor LV function with severe involvement of the interventricular septum (IVS) and reduced motion of the left ventricular posterior wall (LVPW). (b) bi-dimensional apical four chamber view with swirling of SMOG heart chambers as a result of poor myocardial function. The SMOG is enhanced in the right atrium. (c) bi-dimensional apical four chamber view with free tricuspid valve regurgitation (TR) due to lack of cooptation of the tricuspid valve leaflets during systole (marked by a red bar) as a result of critical reduction of right ventricular function and right ventricular enlargement. (d) Right and left ventricular thrombi seen in the short axis apical parasternal view. T1-large right ventricular thrombus, T2&amp;amp;T3-left ventricular thrombi. (e) The color-flow Doppler picture: TR. Free regurgitation of the tricuspid valve shown in modified four chambers apical view. RA-right atrium, RV-right ventricle, LA-left atrium, LV-left ventricle, TR-tricuspid regurgitation color-flow Doppler. D. Photomicrografh demonstrating fibrosis and interstitial inflammation in the heart of patient VI10. a c- post-mortem heart sections (2.7Y). (a) Prominent fibrosis and lymphocytic interstitial inflammation (Hematoxylin Eosin x50). (c) Sub-epicardial inflammation and mild interstitial "myocarditis" (Hematoxylin Eosin x100). (b d)- Fetal heart (VI7) homozygous for p.Tyr747Ter. No inflammatory infiltrate or other histological abnormalities are seen. (b) Normal arrayed myocardium (Hematoxylin Eosin x50). (d) Sub-epicardial region with no histopathological changes. (Hematoxylin Eosin x100). E. Sanger sequencing confirming that the patient VI10, is homozygous for the causative SV c.2241C> G, p.Tyr747Ter in PPP1R13L. F. Segregation of c.2241C> G, p.Y747X in PPP1R13L in the studied family: The affected girl VI10, is homozygous for the causative SV p.Y747X, as are the four fetuses that were aborted. The parents are obligate carriers as shown and, of the two healthy sisters, one carries the wild allele only, and the other is heterozygous for the causative SV.
Suppressed accumulation of Ub in Atg7-/p62-deficient brains.Figure 2.Suppressed accumulation of Ub in Atg7-/p62-deficient brains. (A and B) Quantitative mass spectrometry analysis of P2UBA captured total (A) and isopeptide-linked (B) Ub from the soluble and insoluble fractions of autophagy-deficient brains. Age-matched control Atg7 littermates (Atg7flox/+:nestin-Cre:p62+/−; denoted +) at 6 wk (open circles; n = 4), p62 KO (Atg7flox/flox:p62−/−; denoted −) at 6 wk (closed circles; n = 3), Atg7 KO (Atg7flox/flox:nestin-Cre:p62+/−; denoted −) at 6 wk (closed diamonds; n = 3), or Atg7-/p62-DKO (Atg7flox/flox:nestin-Cre:p62−/−) at 6 wk (closed triangles; n = 3) are shown. Each symbol represents one animal. *, P ≤ 0.05; **, P ≤ 0.01; ***, P ≤ 0.005.
The chemoattractant‐induced Ca2+ influx is orchestrated by changes in pHi and VmCalibrated Vm (left) and pHi (right) changes and Ca2+ signals (middle) evoked by resact.Figure 6A Calibrated Vm (left) and pHi (right) changes and Ca2+ signals (middle) evoked by resact. B Normalized Vm, pHi, and Ca2+ signals evoked by 10 pM resact; the first 600 ms after mixing are shown. The hyperpolarization precedes the pHi increase, whereas the pHi increase precedes the Ca2+ increase. C Latency of the Vm, the pHi, and the Ca2+ signals evoked by various resact concentrations (mean ± SD; n = 3). D Normalized pHi and Ca2+ signals evoked by photorelease of cGMP in sperm loaded with caged cGMP. E Calibrated Vm and Ca2+ signals evoked by 1 nM resact; the threshold voltage (Vthr) for the Ca2+ influx was deduced from the latency of the Ca2+ signal. F Calibrated pHi and Ca2+ signals evoked by 1 nM resact; the threshold pHi (pHthr) at which the Ca2+ influx commences was deduced from the latency of the Ca2+ signal. G Linear relationship between pHthr and Vthr for activation of Ca2+ influx by various resact concentrations (data derived from Supplementary Fig S6; mean ± SD; n ≥ 3).
Fig.Figure 3(A) Representative images of necrotic cell death (SYTOX orange - red fluorescence) at 2-, 24- and 48-hours post exposure to 10ng/mL TcdB in control Bmal1f/f-EsrCRE enteroids. Scale bar = 250μm. (B) Quantitative analysis of fluorescent intensity from SYTOX orange in control Bmal1f/f-EsrCRE enteroids without tamoxifen treatment. (C) Representative images of necrotic cell death (SYTOX orange) at 2-, 24- and 48-hours post exposure to 10ng/mL TcdB in tamoxifen-treated circadian arrhythmic Bmal1f/f-EsrCRE enteroids. Scale bar = 250μm. (D) Quantitative analysis of fluorescent intensity from SYTOX orange in tamoxifen-treated circadian arrhythmic Bmal1f/f-EsrCRE enteroids.
Figure 2(A, B and C) Polyphenols inhibits the autophosphorylation of RhpS-FL protein. Inverted membrane vesicles containing RhpS-FL protein were phosphorylated with 10-μCi [γ-32P]-ATP. Polyphenols TA (A), PGG (B), or EGCG (C) were added into the mixture for 20 min at different concentrations before stopping the reaction. The phosphorylated proteins were separated by 12% SDS-PAGE. After electrophoresis, the SDS-PAGE gels were dried with gel-dryer and then exposed to a medical X-ray film overnight. This experiment was repeated twice, yielding similar results. Data information: the reaction was stopped by adding 5 × loading buffer before SDS-PAGE. Abbreviation is as follows: CBB, coomassie bright blue stain; CFU, colony-forming unit. (D, E and F) Polyphenols inhibit the phosphatase activity of RhpS. The GST-RhpR was phosphorylated by adding 5-μM PSPPH_3550c protein as well as 10-μCi [γ-32P]-ATP for 10 minutes. The RhpS-FL protein was treated in the presence of different concentrations of TA (D), PGG (E), or EGCG (F) for 10 min. Then, the full-length RhpS protein was added into the mixture phosphorylated GST-RhpR for 1 hour before stopping the reaction. The phosphorylated proteins were separated by 12% SDS-PAGE. After electrophoresis, the SDS-PAGE gels were dried with gel-dryer and then exposed to a medical X-ray film overnight. This experiment was repeated twice, yielding similar results. Data information: the reaction was stopped by adding 5 × loading buffer before SDS-PAGE. Abbreviation is as follows: CBB, coomassie bright blue stain; CFU, colony-forming unit. (G) Quantification of the band intensities of (D, E and F). The intensities of the phosphorylation bands were calculated using Image J software. The individual data points were shown (n=2 biological replicates). (H) Venn diagram of TA/PGG/EGCG-inhibited genes and RhpS-activated genes at 4-fold cut-off. (I, J and K) Polyphenols inhibits the virulence levels and in planta growth of Psph in bean plants. Bacterial virulence levels were estimated by inoculating Psph strains with or without polyphenols onto host bean plants. Disease symptoms were recorded 5 days after inoculation. Leaf disks (1 cm2) were removed 5 days after inoculation and diluted in sterile water to count bacterial CFUs. The experiment was repeated three times. Data information: , * indicate significant differences between mock group and strains under the different test conditions as indicated. (Student's t test. *, P ≤ 0.05, **, P ≤ 0.01, and ***, P ≤ 0.001). Error bars represent standard deviations (n=3 biological replicates). (L) Ion leakage assay of Pto DC3000 infection of bean plants with or without indicating polyphenols. The error bars represent standard deviations (n=3 biological replicates). Data information: , * indicate significant differences between mock group and strains under the different test conditions as indicated. (Student's t test. *, P ≤ 0.05, **, P ≤ 0.01, and ***, P ≤ 0.001). Error bars represent standard deviations (n=3 biological replicates).
Fig.Figure 8GA promotes PLDα6 translocation from cytosol to the nucleus, resulting in an increase of PA in nuclear membranes. PA binds to GID1, tethers it to the membrane, facilitates its nuclear translocation and the degradation of the suppressor SLR1, enhancing rice response to GA. PLs, phospholipids.
Tpm protects non-oxidized but not oxidized F-actin from cofilin-induced severing.Figure 4A. Time-lapse images of filaments, oxidized or not, bare or Tpm-saturated, exposed to 1 µM mCherry-cofilin-1, from time t=0 onwards. B. Nucleation of the first cofilin domain onto 5 µm-long Tpm-saturated actin filaments. Filaments are exposed to 1 µM mCherry-cofilin from time t=0 onwards. N = 50 filaments from 1 experiment for each condition. P-value = 4.10-15 (log-rank test). Data information: (B Thick solid and dashed lines are survival fractions calculated from the experimental data. Thin grey lines are single exponential fits. 95% confidence intervals are shown as shaded surfaces. C. Growth rate of single cofilin domains, normalized by the cofilin concentration. Filaments saturated by Tpm during aging (Figure 1A) were then exposed to cofilin, along with 0-100 nM nGr-Tpm1.8 to test the competition between the two soluble proteins. Note the scale difference for oxidized filaments. Bars: Mean and S.D. Number of experiments, first to last condition: 2, 1, 1, 3 and 1. D,E. Filament severing rate at single cofilin domains. Time t=0 is defined for every domain as the frame on which they nucleate. N = 163 (2 experiments), 180 (4 experiments), 116 (3 experiments), 203 (3 experiments) domains for bare actin (100 nM mCherry-cofilin-1), non-oxidized Tpm-saturated (1 µM mCherry-cofilin-1), oxidized Tpm-saturated filaments (100 nM mCherry-cofilin-1), and bare oxidized actin (10, 20, 30 nM mCherry-cofilin-1), respectively. Data information D, E) Thick solid and dashed lines are survival fractions calculated from the experimental data. Thin grey lines are single exponential fits. 95% confidence intervals are shown as shaded surfaces.
Figure 3Western blot analysis of p-Stat5 in livers of 9-week-old mice (n=3 per group, 3 independent repeats), with quantitation of the ratio of p- to total Stat5 shown below the blot. Hsp90, loading control for Western blot analysis. qPCR analysis of p-Stat5-associated growth genes in the livers of 9-week-old mice (n=6 per group, 2 independent repeats). Ribosomal L32, loading control for qPCR analysis. Z ambulatory activity of 9-week-old male mice as measured over 24 hr (n=4 males per group). Blood glucose levels in 9-week-old mice after 6 hr fasting (n=6-10 per group). serum insulin levels in 9-week-old mice after 6 hr fasting (n=6-10 per group). serum triglyceride (TG) levels in 9-week-old mice after 6 hr fasting (n=6-10 per group). serum cholesterol (CHOL) levels in 9-week-old mice after 6 hr fasting (n=6-10 per group). H&E images of inguinal white adipose tissue (iWAT) from 8-week-old mice (n=3 per group, 2 independent repeats). qPCR analysis of browning-related genes in iWAT (n=3-6 per group). Ribosomal L32, loading control for qPCR analysis. Western blot analysis of Ucp1 in iWAT of 8-week-old mice (n=3-4 per group, 3 independent repeats). Hsp90, loading control for Western blot analysis. Weight gain curve of male mice after 60% high fat diet (HFD) starting at 5 weeks of age (n=4 per group, 2 independent repeats). Adipose tissue weight normalized to body weight in male mice following 9 weeks of HFD feeding (n=4 per group).
Figure 5(A) Cecum of mice treated with or without antibiotics for 6 weeks (B) Body weight of animals fed to CC or HFD and treated with or without antibiotics for 6 weeks. Animals were fed to CC or HFD during the experiment. (n=8 HF and CC control, n=18 HF and CC + antibiotic; HFD control vs. HF antibiotic: Student t-test *p<0.05; HF antibiotic vs. CC antibiotic: unpaired, two-tailed Student t-test #p<0.05). (C) Gene expression of Pparγ and PPARγ target genes in the liver of mice fed to CC or HFD for 6 weeks and simultaneously treated with an antibiotic cocktail (n=4 for each antibiotic untreated group, n=9 for each antibiotics treated group, per ZT; ZT0 and ZT12 two-way ANOVA, post hoc Holm-Sidak comparisons *p<0.05 , ** <0.001, ***p <0.001 ).
Identification of metaphase phosphorylation sites in M18BP1-1 by mass spectrometry A, B) Metaphase binding of M18BP1-1 to CENP-C requires phosphorylation.Figure 4A, B) Metaphase binding of M18BP1-1 to CENP-C requires phosphorylation. Either full-length Myc-M18BP1-1 (A) or Myc-M18BP1-1161-580 (B) was immunoprecipitated from metaphase extract. Half of the immunoprecipitate was treated with λ-protein phosphatase (+ LPPase) to assess whether binding to CENP-C required phosphorylation. Immunoprecipitation with an equivalent amount of mouse IgG served as a negative control. Immunoblotted species is indicated at left. C) Cdk inhibition with flavopiridol prevents M18BP1-1161-580 localization at metaphase centromeres. Representative images showing Myc-M18BP1-1161-580 localization at sperm centromeres in metaphase extract depleted of endogenous M18BP1 following treatment with various mitotic kinase inhibitors. Inhibitor treatment is indicated at left, immunolocalized protein is indicated above. Scale bar, 10 μm. Insets are magnified 3X. D) Schematic of phosphorylation sites in M18BP1-1161-580 mutated for this study. M18BP1-1 residue numbers indicated above. Positions of phosphorylation sites are indicated by orange lines and labels below. Bold indicates consensus Cdk phosphorylation sites. E) Quantification of immunofluorescence experiments examining localization of M18BP1-1161-580 phosphorylation site mutants to sperm centromeres in metaphase extract depleted of endogenous M18BP1. Graph shows mean centromere intensity ± SEM of three independent experiments normalized to the WT condition. Significance determined by Welch's unpaired two-tailed t-test, * p<0.05, ** p<0.005.
Figure 5A, Exemplary ABR traces (Click 100dB) from one OtofI515T/I515T mouse recorded at indicated bullatemperatures during local heating. Note that ABRs never disappeared completely, but wave I amplitude changed reversibly with temperature. B,C, ABR wave I amplitudes in OtofI515T/I515T (A, Click 100dB) and Otof+/+ mice (B, Click 80dB) decreased with increasing temperature in the bulla. Each color represents a different experiment, dashed lines are line fits. Open symbols indicate the beginning of the experiments; subsequent recordings are connected by lines. The four indicated data points in B correspond to ABRs in A. D, Explanted organ of Corti from an Otof+/+ mouse at P4 after two days in vitro (DIV2) at 37°C immunostained against otoferlin (magenta) and Vglut3 (green). Note the intense immunostaining of otoferlin at the plasma membrane. Scale bar 10 µm.E-J, Explanted organs of Corti from Otof-/- mice at P4 were transfected by GeneGun with otoferlin cDNA and eGFP and immunostained at DIV2.E, Example cell transfected with wild-type mouseotoferlin cDNA.F,G, Representative cells transfected with mouseotoferlin including the 20 amino acids of the RXR motif (see Fig EV4). Cells in G were incubated at 38.5°C for 30 min prior to fixation. The RXR-otoferlin transfected cells show a membrane localization of otoferlin surrounding the Vglut3 immunofluorescence/eGFP fluorescence at the basal pole of the cells (arrows), similar as in controls (A,B).H,J, Both the human RXR motif and the Ile515Thr mutation were introduced in mouse cDNA, and cells were incubated at 37°C (H) or for 30min at 38.5°C (J) before fixation. Here, green fluorescence surrounds the otoferlin immunofluorescence (arrows), suggesting loss of otoferlin from the plasma membrane.K, Quantification of the relative plasma membrane levels of otoferlin (as in Fig 1) revealed normal plasma membrane abundance when the human RXR motif was present, but a strong reduction for otoferlin with RXR and Ile515Thr (individual cells; mean ±SEM; t-test).
Figure 5(A) Western blotting analysis of FadA, E-cadherin (CDH1), Annexin A1 (ANXA1) and β-catenin in DLD1 cells following incubation with FadAc for 15 or 120 min. C, untreated cells. β-actin was included as an internal control. The experiment was repeated three times. (B) Co-immunoprecipitation with Annexin A1. DLD1 cell lysates were incubated with FadAc for 15 or 120 min and mixed with agarose beads conjugated with rabbit anti-Annexin A1 polyclonal antibody (α-Annexin A1) or control rabbit IgG. FadA, E-cadherin (CDH1), Annexin A1 (ANXA1) and β-catenin in the eluates were detected by Western blot. C, untreated control. The experiment was repeated three times. (C) Co-immunoprecipiation with FadA. DLD1 cell lysates were incubated with FadAc for 15 or 120 min and mixed with agarose beads conjugated with mouse anti-FadA monoclonal antibody (α-FadA) or control mouse IgG. FadA, E-cadherin (CDH1), Annexin A1 (ANXA1) and β-catenin in the eluates were detected by Western blot. The experiment was repeated three times. (D) Confocal microscopy analysis of 10C cells either untreated (top panel) or following incubation with CFSE-labeled F. nucleatum 12230 (red, bottom panel) for 3 hrs and then immunofluorescent-stained for Annexin A1 (green) and E-cadherin (blue). Images are 1200x magnification. A side view of the enlarged image is shown on the far right. Note the enhanced expression of Annexin A1 in the F. nucleatum-bound cells and the co-localization of Annexin A1, E-cadherin and F. nucleatum on the cell membranes (arrows). The experiment was repeated more than three times. Scale bar, 500 nm. (E) Confocal microscopy analysis of 10C cells following incubation with Alexa Fluor™ 488-conjugated BSA, mFadA, or FadAc (red) for 1 hr and immuno-staining of Annexin A1 (green) and E-cadherin (blue). Images are 1200x magnification. Note the enhanced expression of Annexin A1 and its co-localization with E-cadherin in the presence of FadAc (arrows), but not with BSA and mFadA. The experiment was repeated twice. The side views are shown to the right and bottom of each image. Scale bar, 500 nm.
Fig.Figure 7A: Body weight was measured in control and siELDR treated mice. n=5 animal per group B: Representative images of tumors in control and treatment groups. C: Tumors were measured using a slide caliper and tumor volumes were calculated. Arrow indicates starting point siELDR treatment. n=5 animal per group and tumor volume presented as the mean ± SD D: ELDR knockdown was examined by analyzing expression of ELDR in treated tumors compared to the control tumors. 18S rRNA gene was used as internal control. n=5 animal per group and 3 technical replicates from each tumor. E: Control or siELDR treated tumor lysates were subjected to Western blot analysis for EGFR and Cyclin E1expression using specific antibodies and representative bands are shown. The blot was reprobed with an antibody against Actin for normalization. Right panels show quantitation. n= 3 biological replicates from each tumor F: OSCC-PDX tissue was implanted subcutaneously into the flank of NSG mice. When the tumor volume reached >70 mm3, mice were divided into two groups. 10µg of siELDR or control oligoes were injected intratumorally as described above. Body weight was measured in control and siELDR treated mice. n=5 animal per group G: Representative images of OSCC-PDX tumors in control and treatment groups. H: PDX tumors were measured using a slide caliper and tumor volumes were calculated. n=5 animal per group and tumor volume presented as the mean ± SD I: ELDR knockdown was examined by analyzing expression of ELDR in treated OSCC-PDX tumors compared to the control tumors. 18S gene was used as internal control. n=5 animal per group and 3 technical replicates presented as the mean ± SD
Figure 1(A) It is unclear how genetic circuits (centre) tune phenotypic variability in a bacterial population in response to genetic perturbation, environmental stress and history (left) to modulate the fraction of cells that activate a given pathway (right). (B) Schematic of the σV circuit. In its inactive form σV is bound to its anti-sigma factor RsiV. If there is lysozyme present in the environment, RsiV binds to lysozyme and undergoes a conformational change. Only then the proteases SipS and RasP can cleave RsiV to release σV. Once σV is released from RsiV it can bind to RNA polymerase to redirect transcription to the σV regulon. σV can initiate transcription of its own operon which includes sigV, rsiV, oatA (one of the main lysozyme resistance genes) and yrhK (unknown function). (C) Time-lapse microscopy of cells containing a PsigV-YFP promoter reporter reveals heterogeneous activation of σV in response to lysozyme stress. The stress (red line) was added between the 200 mins and 300 min time points (at 240 min). The red arrow highlights a cell with a delayed activation of σV. Scale bar: 5 μm. (D) Time traces of mean YFP fluorescence per cell. Each trace represents a single cell lineage's response to 1 µg/ml lysozyme. (109 traces from two independent experiments). Lysozyme added at the black dashed line. (E) Figure D replotted to allow examination of variable activation times. (F) The observed heterogeneity is reduced with increasing stress levels. Each line represents the cumulative fraction of cells (N=~50) with PsigV-YFP values that are higher than the half maximum of their final values (representing cells that have activated). (G) The fold change in mean YFP fluorescence increases with increasing stress levels, shown for two biological repeats (adjacent boxplots). Each day's fold change distribution consisted of >40 manually corrected single-cell traces. On each box, the central mark indicates the median, and the bottom and top edges of the box indicate the 25th and 75th percentiles, respectively. The whiskers extend to the most extreme data points not considered outliers.
Figure 4A Dot plot showing the expression level of genes belonging to the γδ TCR-induced signature across DN3a, DN3b γδ+, DN4γδ+, DN3b γδ- and DN4γδ- subsets of Dataset 1. The γδ TCR-induced signature was defined by comparing the transcriptome of DN3b γδ- and DN3b γδ+ cells (see Methods). B, C AUCell scores for the γδ TCR-induced signature among the UMAP plot of cells corresponding to Dataset 1 (B) and Dataset 2 (C). As shown in Fig EV2, Dataset 2 corresponds to DN-enriched scRNAseq data merged with whole thymus scRNAseq data. D Dot plot showing the expression level of genes belonging to the γδ TCR-induced signature across the cell subsets corresponding to Dataset 2. Based on the gene set that was specifically upregulated during the DPsmall → DPCD69+/SP transition (see Fig EV3B), it allowed to subdivide the γδ TCR-induced signature into a 'γδ TCR only' signature and a 'αβ and γδ TCR shared' signature E, F AUCell scores for the 'αβ and γδ TCR shared' signature (left panel) and for the 'γδ TCR only' signature (right panel) among the UMAP plot of cells corresponding to Datasets 1 (E) and 2 (F).
Structure of the TbIFT22/74/81 complex A.Figure 2A. Domain organization of IFT81, IFT74 and IFT22. Numbers refer to the T. brucei protein sequence and indicate different constructs used in this study. The part of the IFT81/74 sequence shown in shaded colors is not part of the construct used for structure determination. Coiled-coil boundaries are depicted based on the structure (ccI-ccVI) or prediction from the PCOILS webserver (cc). (CH = calponin homology, cc = coiled-coil). B. Crystal structure of TbIFT22/7479-401/811-450 in two perpendicular orientations shown in cartoon representation. GTP is shown as a stick model. IFT22 is depicted in green, IFT74 in orange and IFT81 in grey. Coiled-coils are labeled ccI-ccVI. C. Zoomed-in view of the N-terminal TbIFT81 CH domain (grey) superposed onto the CrIFT81 CH domain (brick-red). Basic tubulin-binding residues are highlighted in yellow and light orange, respectively. D. Zoomed-in view of the IFT22-binding site on IFT74/81 ccVI with ordered switch regions of IFT22 depicted in yellow.