EMBO/sd-character-level-ner huggingface dataset:
Rheotaxis of human sperm in viscous media and in the presence of progesterone.Figure 6Spider-web plot of the mean (± SD) angular frequencies (binning: 315°-45°, 45°-135°, 135°-225°, and 225°-315°; 403 sperm; 3 experiments) of human sperm swimming in buffer fortified with 0.2 % (w/v) methyl cellulose in the presence of a fluid flow. Spider-web plot of the mean (± SD) angular frequencies (520 sperm; 3 experiments) of human CATSPER2-/- sperm swimming in buffer fortified with 0.2 % (w/v) methyl cellulose in the presence of a fluid flow. Spider-web plot of the mean (± SD) angular frequencies (binning: 315°-45°, 45°-135°, 135°-225°, and 225°-315°; 454 sperm; 3 experiments) of human sperm swimming in buffer fortified with 100 nM progesterone in the presence of a fluid flow. Spider-web plot of the mean (± SD) angular frequencies (372 sperm; 3 experiments) of human CATSPER2-/- sperm swimming in buffer fortified with 100 nM progesterone in the presence of a fluid flow.
Figure 7SARS-CoV-2 infects a subpopulation of enterocytes in human mini-gut organoids. Upon infection, enterocytes mount a pro-inflammatory response characterized by the upregulation of NFκB and TNF. Bystander cells respond to secreted IFN and upregulate the expression of ISGs. SARS-CoV-2 infection induces the downregulation of ACE2 expression and interferes with IFN-mediated signalling in infected cells. Created with BioRender.
CENATAC promotes error-free chromosome segregation.Figure 2Quantification of chromosome segregation errors of patient and control lymphoblasts expressing H2B-mNeon (four biological replicates, >200 cells in total per condition). Representative images of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells depleted of GAPDH (upper) or CENATAC (middle and lower) with or without re-expression of CENATAC variants as indicated. IAA, 3-indoleacetic acid. Scale bar, 10 μm. Quantification of mitotic defects as in (B) of H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells treated as indicated (three or five biological replicates, >85 cells in total per condition). For 2xZF the four zinc-finger cysteines were mutated to alanines; for Δ1-4 the corresponding motif was removed. Representative stills of HeLaEGFP-AID-CENATAC cells expressing H2B-mNeon and depleted of CENATAC. Microtubules were visualized with SiR-Tubulin. Arrowheads and arrows indicate non-congressed chromosomes and supernumerary spindle poles, respectively. Scale bar, 5 μm. Time in hours. See Figure EV2 for the control condition. See also Movies EV1 and EV2. IAA, 3-indoleacetic acid. Quantification of the mitotic phenotype and multipolar spindle formation in time in H2B-mNeon-expressing HeLaEGFP-AID-CENATAC cells treated as in (D) (three biological replicates, >44 cells in total per condition). See also Figure EV2.
Lack of caspase-1/caspase-11 inhibits CNV lesion formation, retinal degeneration, fundus abnormalities and fundus autofluorescence in aged VEGF-Ahyper mice.Figure 11Figure 11: Lack of caspase-1/caspase-11 inhibits CNV lesion formation, retinal degeneration, fundus abnormalities and fundus autofluorescence in aged VEGF-Ahyper mice.A. OCTs in aged VEGF-Ahypermice show retinal degeneration with a thinning of the retina and CNV lesions extending from the choroid into the subretinal space (arrows). OCTs appear normal in age-matched VEGF-Ahyper/CASP1-/-/CASP11-/-mice and CASP1-/-/CASP11-/-mice.B. Fundus autofluorescence imaging shows areas of autofluorescence in the fundus of aged VEGF-Ahypermice, but not in age-matched VEGF-Ahyper/CASP1-/-/CASP11-/-mice and CASP1-/-/CASP11-/-mice.C. Abnormal pigment loss and degenerative changes are observed in the fundus of aged VEGF-Ahypermice, while the fundus of age-matched VEGF-Ahyper/CASP1-/-/CASP11-/-mice and CASP1-/-/CASP11-/-mice does not show these abnormalities.Representative images of 21-months old mice are shown.
Quality marker panels in a weight loss study and literature study.Figure 4Assessment of individual sample quality with respect to the three contamination indices using the online tool at www.plasmaproteomeprofiling.org. Samples with indices that are more than two standard deviations from the mean (horizontal red lines) are flagged as potentially contaminated (red bars and sample numbers). Volcano plot of the proteome comparison of time point 1 vs 4. Proteins of the platelet panel are highlighted in blue and two additional significantly regulated proteins in red. Global correlation map on the left with an inset of the platelet cluster on the right. The two significant outliers of the volcano plot in (B) are marked in red. Platelet panel proteins are highlighted in blue in the inset. Red patches in the global correlation map indicate positive and blue patches negative correlations. Literature analysis of 210 publications using MS-based plasma proteomics to identify new biomarkers. The number of quality markers reported as biomarker candidates in these studies is indicated. Distribution of the reported quality markers according to the three types of likely contaminations. The distribution is shown across studies that report one, two or three proteins of the same quality marker panel.
Oscillations in isotopic labeling of TCA cycle metabolites throughout the cell cycle from [U-13C]-glucose show induced glycolytic flux into TCA cycle in G1/S.Figure 3(a) Experimental scheme for a series of pulse-chase isotope tracing experiments in synchronized cells. (b) Atom tracing of TCA cycle metabolites from [U-13C]-glucose (blue) and [U-13C]-glutamine (red). (c-e) Measured relative fraction of the m+2 labeling of TCA cycle intermediates after feeding [U-13C]-glucose (red; mean and s.d. of n=3), the deconvoluted signal (green), and the expected labeling dynamics considering the loss in synchronization (black; representing TCA cycle oxidation of glucose-derived acetyl-CoA). (c-e) Measured relative fraction of the m+2 labeling of TCA cycle intermediates after feeding [U-13C]-glucose (red; mean and s.d. of n=3), the deconvoluted signal (green), and the expected labeling dynamics considering the loss in synchronization (black; representing TCA cycle oxidation of glucose-derived acetyl-CoA). (c-e) Measured relative fraction of the m+2 labeling of TCA cycle intermediates after feeding [U-13C]-glucose (red; mean and s.d. of n=3), the deconvoluted signal (green), and the expected labeling dynamics considering the loss in synchronization (black; representing TCA cycle oxidation of glucose-derived acetyl-CoA). (f) Oscillations in citrate m+4 labeling after feeding [U-13C]-glutamine (mean and s.d. of n=3). (g) Oscillations in the total citrate concentration throughout the cell cycle (mean and s.d. of n=5). (h) The measured lactate secretion flux in synchronized cells shown in red (mean and s.d. of n=5; in Equation 9;); the deconvoluted secretion flux dynamics, in case of no synchronization loss (green; in Equation 10); and the expected secretion flux based on the deconvoluted fluxes and considering the loss in synchronization, matching the measured fluxes (black; Equation 10).
Figure 4A) Severe onychomycosis in P2 (STIM1 p.L374P). B) PBMC of a healthy donor (HD1) cultured for 6 days in the presence of 6.5 mg/ml C. albicans protein. At day 6, PBMC were restimulated with PMA and ionomycin in the presence of 10 μM GSK-7975A or DMSO for 6 h and CD4+ and CD8+ T cells were analyzed for cytokine production by flow cytometry. Bar graphs represent the mean ± SEM from two independent experiments. Human T cells from two healthy donors, P1 and his mother were expanded and cultured in the presence of C. albicans and IL-2 for 2-4 weeks. (C) T cells were restimulated with PMA and ionomycin for 6 h in the presence or absence of 10 μM GSK-7975A and analyzed for cytokine production by flow cytometry. Bar graphs represent the mean ± SEM from two independent experiments. Human T cells from two healthy donors, P1 and his mother were expanded and cultured in the presence of C. albicans and IL-2 for 2-4 weeks. (D) Fura-2 loaded T cells were stimulated with thapsigargin (TG) in Ca2+-free buffer followed by readdition of 2 mM Ca2+ to induce SOCE. Bar graphs represent the mean ± SEM from two independent experiments.
Movement of the LS‐TVN‐associated tubules is dependent on the microtubule network.Figure 5B) Cells infected with UIS4‐mCherry‐expressing parasites were treated with nocodazole for 1.5 h (top) or cytochalasin D for 30 min (bottom) and imaged by confocal microscopy. Imaging occurred 29 and 24 h post‐infection, respectively. UIS4‐positive tubules, static (top) and dynamic (bottom), are indicated with white arrowheads. Displayed cells are representative of five imaged parasites from at least two different experiments. B) Cells infected with UIS4‐mCherry‐expressing parasites were treated with nocodazole for 1.5 h (top) or cytochalasin D for 30 min (bottom) and imaged by confocal microscopy. Imaging occurred 29 and 24 h post‐infection, respectively. UIS4‐positive tubules, static (top) and dynamic (bottom), are indicated with white arrowheads. Displayed cells are representative of five imaged parasites from at least two different experiments. C) No colocalization between host microtubules and UIS4‐positive tubules is detectable. Infected cells were fixed 25 h post‐infection and stained with antibodies against UIS4 and Tubulin. Scale bars, 10 µm.
KRAS pathway activation in MPM from the cancer genome atlas (TCGA) pan-cancer MPM dataset.Figure 2Molecular and clinical features of the cancer genome atlas (TCGA) pan-cancer MPM patients (n = 87) stratified by the presence of KRAS standalone (n = 10) and combined KRAS/TP53 (n = 7) alterations. Shown are unsupervised hierarchical clustering of n = 86 patients (gene expression data were not available for one patient) by 40 genes significantly overexpressed in KRAS/TP53-altered over KRAS-altered over KRAS/TP53-normal patients (A) and data summaries of mononucleotide change signatures (B), of indices of genomic instability and mutation burden (C), of clinical features Molecular and clinical features of the cancer genome atlas (TCGA) pan-cancer MPM patients (n = 87) stratified by the presence of KRAS standalone (n = 10) and combined KRAS/TP53 (n = 7) alterations. Shown are unsupervised hierarchical clustering of n = 86 patients (gene expression data were not available for one patient) by 40 genes significantly overexpressed in KRAS/TP53-altered over KRAS-altered over KRAS/TP53-normal patients KRAS/TP53/NF2 co-mutation frequency Molecular and clinical features of the cancer genome atlas (TCGA) pan-cancer MPM patients (n = 87) stratified by the presence of KRAS standalone (n = 10) and combined KRAS/TP53 (n = 7) alterations. Shown are unsupervised hierarchical clustering of n = 86 patients (gene expression data were not available for one patient) by 40 genes significantly overexpressed in KRAS/TP53-altered over KRAS-altered over KRAS/TP53-normal patients overall survival (F). G KRAS/TP53 pathway adapted from Matallanas et al (2011) and Tikoo, et al (1994). Color-coded genes were identified by TCGA and PANTHER pathway analyses. PANTHER and Reactome KRAS and TP53 pathways significantly altered in the cancer genome atlas (TCGA) pan-cancer MPM patients. Shown are volcano plot of fold-enrichment versus -log10(probability) (H) PANTHER and Reactome KRAS and TP53 pathways significantly altered in the cancer genome atlas (TCGA) pan-cancer MPM patients. data summary of fold-enrichment of KRAS and TP53 versus all other pathways with fold-enrichment > 0.5 (I).
Figure 6A. Co-immunolocalization against tubulin (magenta) and KNOLLE (green) in root meristematic cells. Nuclei were counterstained with DAPI for the DNA (cyan). Scale bars: 5 μm. B. Quantification of wildtype (WT) and abnormal phragmoplasts. Different letters indicate significant differences in the proportions of the different arrays per category in a Chi-squared test followed by the Marascuilo procedure to identify significant pairwise comparisons. Ten roots were analyzed per genotype. C. Quantification of the different mitotic stages in roots of the different genotypes. Different letters indicate significant differences in the proportions of the different arrays per category in a Chi-squared test followed by the Marascuilo procedure to identify significant pairwise comparisons. Ten roots were analyzed per genotype.
Figure 5A Representative example of ABR traces obtained at 4w from a WT, Syne4-/- mouse, and Syne4-/- mouse injected with AAV.Syne4 in response to an 18 kHz stimulus. B ABR thresholds at 4w of WT, Syne4-/-, Syne4-/- mice injected with AAV.Syne4, and Syne4-/- mice injected with AAV.GFP, n=7 for WT, n=8 for Syne4-/-, n=20 for Syne4-/- + AAV.Syne4, n=6 for Syne4-/- + AAV.GFP. C Quantification of P1-N1 amplitude delta from (B), n=4 for WT, n=4 for Syne4-/-, n=7 for Syne4-/- + AAV.Syne4. D Quantification of P1 latency from (B), n=4 for WT, n=2 for Syne4-/-, n=7 for Syne4-/- + AAV.Syne4. E DPOAE thresholds at 4w, n=6 for WT, n=5 for Syne4-/-, n=6 for Syne4-/- + AAV.Syne4. F ABR threshold at 12w, n=6 for WT, n=8 for Syne4-/-, n=16 for Syne4-/- + AAV.Syne4, n=5 for Syne4-/- + AAV.GFP.
Figure 2A. Mass spectrometry analysis of TRIM46-associated proteins. Whole-cell extracts from MCF-7 cells stably expressing FLAG-TRIM46 were subjected to affinity purification with anti-FLAG immobilized on the agarose beads. The purified protein complex was resolved on SDS-PAGE and silver-stained. The bands were retrieved and analyzed by mass spectrometry. B. MCF-7 cells were transfected with a control vector or FLAG-TRIM46 for 40 h and treated with DMSO or MG132 (2μM) for 10h. Cellular lysates were then collected for western blotting with antibodies against the indicated proteins. C. MCF-7 cells were transfected with control vector or FLAG-TRIM46 for 48 h. Whole-cell lysates were prepared, and immunoprecipitation was performed with anti-FLAG followed by immunoblotting with antibodies against indicated proteins (top). Immunoprecipitation assays in MCF-7 cells with anti-TRIM46 followed by immunoblotting with antibodies against the indicated proteins (bottom). D. Schematic diagrams of TRIM46 deletion mutants (left). Coomassie brilliant blue (CBB) staining of GST-fused proteins as indicated (right). GST-FL was shown with the arrow. E. GST pull-down experiments were performed with bacterially expressed GST-fused proteins as shown and in vitro transcribed/translated full-length HDAC1. F. Schematic diagrams of HDAC1 deletion mutants. GST pull-down experiments were performed with bacterially expressed GST-fused proteins as indicated and in vitro transcribed/translated TRIM46.
The CARS-CaMKK2-AMPK axis promotes cell survival when cystine is eliminated (A) The crystal violet assay was performed in cystine-deficient medium-cultured 293T, RCC4 and SK-MES cells with or without 1 µg/ml STO-609 for 24 h.Figure 4(A) The crystal violet assay was performed in cystine-deficient medium-cultured 293T, RCC4 and SK-MES cells with or without 1 µg/ml STO-609 for 24 h. (B) The cell death level was determined in 293T cells with the same treatment conditions as in Figure 4A. Data are presented as the mean (± SD) of three independent experiments. NS, not significant; *P < 0.05 [two-tailed Student's t-test], compared with the indicated groups. (C, D) The crystal violet assay (C) and apoptosis rate assay (D) were performed in 293T cells transfected with shRNAs targeting NTC, CARS, CaMKK2 or AMPKγ2 and further treated with cystine-deficient medium for 24 h with or without 1 mM AICAR. Data are presented as the mean (± SD) of three independent experiments. NS, not significant; *P < 0.05 [two-tailed Student's t-test], compared with the indicated groups. (E) WB analysis of CARS, CaMKK2 and AMPKγ2 protein expression in RCC4, SK-MES, 293T, 786-O, NCI-1650, and HT-1080 cells. Actin served as the loading control. (F WB analysis of p-AMPK, total AMPK, CARS, AMPKγ2, and CaMKK2 protein expression with 786-O cells transfected with Flag-EV, Flag-CARS, Flag-CaMKK2 or Flag-AMPKγ2 and further treated with cystine-deficient medium for 8 h. Actin served as the loading control. Data are presented as the mean (± SD) of three independent experiments. NS, not significant; *P < 0.05 [two-tailed Student's t-test], compared with the indicated groups. G) crystal violet assay were performed with 786-O cells transfected with Flag-EV, Flag-CARS, Flag-CaMKK2 or Flag-AMPKγ2 and further treated with cystine-deficient medium for 8 h. Actin served as the loading control. After scanning, 20% glacial acetic acid was added to dissolve the crystal violet, and the absorbance of each well was measured at 570 nm (OD570) to calculate relative cell viability (G, right). Data are presented as the mean (± SD) of three independent experiments. NS, not significant; *P < 0.05 [two-tailed Student's t-test], compared with the indicated groups.
Time-of-addition study with selected FDA-approved drugs.Fig. 3.Time-of-addition study with selected FDA-approved drugs.Five FDA-approved drugs were analyzed by time-course experiments to determine the stage in the MERS-CoV life cycle that is inhibited by the drugs. Vero cells were infected at a multiplicity of infection (MOI) of 5 with MERS-CoV, and FDA-approved drugs were administered at six-time points prior to or post-infection as indicated. Drug concentrations were higher than the 90% inhibitory concentration (IC90) values of the drugs, and chloroquine was used as an early stage infection inhibitor control.
a) Immunoblots for the indicated proteins in MEFs treated with tamoxifen (Tx) or lindane (Lind) in the absence or presence of lysosomal protease inhibitors (PI).figf4(a) Immunoblots for the indicated proteins in MEFs treated with tamoxifen (Tx) or lindane (Lind) in the absence or presence of lysosomal protease inhibitors (PI). Right: Changes in LC3-II levels relative to those detected in untreated cells (n = 4 independent experiments). (b) Immunofluorescence for Cx43 and LC3 in NRK cells treated as in a in the presence or absence of chloroquine (CQ) for 3 h. Right: Quantification of the average number of LC3-positive puncta per cell (n = 3 wells, 3 independent experiments, >30 cells per experiment). (c) Time course of changes in the average LC3-positive puncta per cell after addition of lindane to control NRK cells. (d) Fluorescence images of WT or Cx43−/− MOBs transfected with mCherry-GFP-LC3 and incubated or not with tamoxifen or lindane. Bottom: Quantification of autophagolysosomes (n = 3 wells, 3 independent experiments, >50 cells per experiment). (e) Immunostaining for Atg16 and Cx43 in MEFs treated with the indicated compounds. Representative images as merged channels are shown. Right: quantification of the average of cytosolic Atg16-positive puncta per cell (n = 3 wells, 3 independent experiments, >30 cells per experiment). (f) Immunofluorescence for LC3 and Atg16 in NRK cells expressing GFP-Cx43 treated with lindane and untreated. Single channel images in inverse black and white and merged colour images are shown. Outlined areas are shown at higher magnification. Arrows: double (yellow) and triple (white) co-localization. (g,h) Immunostaining for Atg16 in Cx43 knocked down (KD) (g) or knocked out (−/−) (h) cells. Right: quantification of the average of cytosolic Atg16 positive puncta per cell (n = 3 wells, 3 independent experiments, >50 cells per experiment). (i) Immunoblot for Atg16 and Atg14 in immunoprecipitates (IP) of endogenous Cx43 from WT MEFs maintained in the absence of serum (4 h) or incubated in the presence of tamoxifen or lindane. I: input; FT: flow through. All values are mean + s.e.m and differences from untreated cells are significant for *P 0.01. Scale bars: 5 μm. Uncropped images of blots are shown in Supplementary Fig. 9.
cGAMP-VLPs pseudotyped with IAV HA induce neutralising antibodies and confer protection following IAV infection.Figure 5A, B. VLPs pseudotyped with IAV HA induce neutralising antibodies. Two (A) or three (B) weeks after immunisation with the indicated doses of VLPs, sera were collected, heat-inactivated, and titres of antibodies capable of neutralising an IAV expressing a matched HA protein were determined by micro-neutralisation (MN) assay. The dotted line shows the limit of detection (LOD). C, D. Low doses of cGAMP-HA-VLPs confer protection following IAV challenge. One month after immunisation with the indicated doses of VLPs, animals were infected with 104 TCID50 of IAV PR8 virus. Weight loss was monitored over the following eleven days and is shown as a percentage of starting weight (C, upper graph shows mean and lower graphs show individual mice for each condition). Animals approaching the humane end-point of 20% weight loss were culled and survival to end-point curves are shown in (D).
Fig.Figure 7(A-B) Grip force of dominant or non-dominant arm in iron-deficient cancer patients, expressed in percentage of baseline force (A) and absolute values normalized to height (B) before/after single dose of iron carboxymaltose (15mg/kg, 7 subjects). Data information: For all data, n represents In graph (A), the boxes represent the range of values with the median value being the central band and whiskers the SEM. (C) Working model: C26 tumor-bearing mice present alterations of key iron metabolism proteins such as the downregulation of TFR1 and the upregulation FT in the skeletal muscle. Decreased cytosolic aconitase activity and the stabilization of IRP2 indicate a low iron status. However, IRP activity is hampered by oxidative stress and is no longer able to regulate TFR and FT (indicated by dashed lines). As a consequence, mitochondrial iron loading is low, and the decrease activity of iron-depending enzymes negatively affect the TCA cycle and the electron transport chain, resulting in decreased ATP production, AMPK activation and muscle atrophy. Iron supplementation replenishes the mitochondrial iron pool and prevents mitochondrial dysfunction. Notably, it restores TCA cycle and electron transport chain activity resulting in higher ATP production, deactivation of AMPK and preserved muscle mass.
Figure 3A B. SEC-MALS analysis of His-GFP-spMis18fl and His-spMis18ΔC, respectively. Refractive index (RI, left Y-axis) and molecular mass (kDa, right Y-axis) profiles show that both His-GFP-spMis18fl (predicted MW of a monomer is 51.97 kDa) and His-spMis18ΔC (Predicted MW of a monomer 21.8 kDa) predominantly exist as tetramers (187.6 kDa and 78.6 kDa, respectively) with a small population of dimer (128.5 kDa and 45.8 kDa, respectively). C. SEC profile of a sample containing an equimolar mixture of purified His-GFP-spMis18C-term-α and His-spMis18MeDiY (upper panel) and SDS-PAGE analysis of SEC-fractions (bottom panel). His-GFP-spMis18C-term-α and His-spMis18MeDiY eluted separately at 12.3 and 15.3 ml, respectively, demonstrating the inability of these domains to interact with each other. D. SEC-MALS analysis of His-GFP-spMis18C-term-α shows that it exists as a homotrimer with a measured molecular weight of 119.8 kDa. (Theoretically calculated MW of a monomer is 38.3 kDa).