EMBO/sd-character-level-ner huggingface dataset:
Distinct genomic profiles of cells from individuals of Back versus White ancestries are accompanied by signs of genomic admixture and variation.Figure 1(A) Principal Component Analysis (PCA) based on 53,837 single nucleotide polymorphisms (SNPs) markers of 62 foreskin donors assessed by microarray chip hybridization (via Illumina Human Omni2.5). PLINK (Package: PLINK1.07) and GCTA analysis tools were used for genetic distance analysis. The first two components (PC1 and PC2) are plotted and explain 5.1% of the variance. Dotted line corresponds to eigenvectors at 0. Each point represents a foreskin donor. Points are labeled and grouped according to self-reported donors' country of origin. (B) Admixture analysis of the indicated HKC strains of Black versus White individuals, on the basis of the SNP genotype dataset with the simplest assumptions of two ancestries (K = 2). On the y-axis admixture proportions are represented as grey and black bars. On the x-axis, individual samples are reported. Dashed lines delimit Black individuals with more than 20% admixture of the other ancestry.
Figure 1(A) Inhibitory pairs showing the inhibitory mRNA codons (red) and the optimal codons (green). Schematic representation of the in vitro elongation reactions performed using the reconstituted yeast translation system. Pelleted 80S initiation complexes (3 nM) are incubated with aminoacyl-tRNAs (15 to 25 nM), elongation factors (1 µM), GTP, and ATP. Reactions are quenched with KOH and the products resolved by electrophoretic TLCs. (B) Representative eTLCs (left) and corresponding elongation kinetics (right) for the CGA-CGA inhibitory pair (red) and the CGC optimal pair (green). Product formation is normalized to the fraction of Met ICs that form Met-Puro when reacted with puromycin (Fig EV1A). (C) Representative eTLCs (left) and corresponding elongation kinetics (right) for the CGA-CCG inhibitory pair (red) and the CGC-CCA optimal pair (green). Product formation is normalized to the fraction of Met ICs that form Met-Puro when reacted with puromycin (Fig EV1A).
Figure 4(A) Nuclear localised Tum-GFP becomes cytoplasmic in mitotic cells, including a distinct plasma membrane localisation (arrows). Note also localisation to the cytokinetic ring (asterisk) and remnant mid-bodies/ring canals in interphase cells. Quantification shown on the right (n > 7 independent samples per genotype; mean +/- 1 S.D. shown). Scale bars ~2µm. (B) A stripe of expression of ptc.Gal4 UAS.tum-RNAi in the wing disc leads to basally extruded cells that undergo apoptosis, marked by Dcp1 immunostaining, similar to UAS.pbl-RNAi. Quantification shown on the right (n > 10 independent samples per genotype; mean +/- 1 S.D. shown). Scale bars ~20µm. (C) Phosphorylated Myosin-II Regulatory Light Chain (p-MLC; red) detected by antibody staining reveals high levels around the cortex of rounded mitotic cells in wild-type wing epithelial cells, but not those cells homozygous mutant for tum347, marked by expression of GFP in single-celled clones (MARCM system). pH3 staining (blue) marks mitotic cell chromosomes. Arrow indicates a GFP-positive single cell tum347 mutant clone. Quantification shown on the right (n > 3 independent samples per genotype; mean +/- 1 S.D. shown). Scale bars ~20µm.
SARS-CoV-2 S1 RBD protein model.Figure 3.SARS-CoV-2 S1 RBD protein model.Basic amino acids that are solvent accessible on the surface are indicated (dark blue); these can be observed to form a continuous patch.
Figure 3(A) Normalised amino-acid concentrations in cells grown in EMM without (grey) or with arginine (red). For each condition, four independent samples were analysed. Concentrations are presented relative to the mean value for the given amino acid in EMM medium. *Ornithine (Orn) is abbreviated as O. The central band indicates the median, the upper and lower limits of the box indicate first and third quartiles, and the whiskers show the most extreme data, limited to 1.5-time interquartile range. (B) Schematic relationship between alpha-ketoglutarate (α-KG) and arginine (R) synthesis (red arrows) and catabolism (blue arrows). Arginine is used to synthesize proline (P), glutamic acid (E), glutamine (Q) and lysine (K). The enzymatic roles of Car1, Car2 and Car3 are indicated. (C) Growth curves of strains deleted for car1, car2 or car3, and a wild-type control. Strains were grown in EMM (black), EMM with antimycin A (red), EMM with arginine (light blue) or EMM with both arginine and antimycin A (dark blue) as indicated. (D) Growth curves of strains deleted for car2 (top) or car3 (bottom). Strains were grown in EMM (black), EMM with antimycin A (red), EMM with arginine and antimycin A (dark blue), EMM with mix of all amino acids and antimycin A (bright blue), and EMM with antimycin A and each individual amino acid from the mix (grey). (E) Growth curves of wild-type control (WT) and car2 deletion strain (Δcar2). Strains were grown in EMM media with antimycin A and with either a mix of all amino acids (+AA mix) or different combinations of lysine (K), glutamine (Q), glutamic acid (E), or arginine (R) as indicated. Dashed line: time point where wild-type strain saturates in EMM with amino-acid mix.
Figure 4A) U2OS cells were treated as in 2B after which mRNA was isolated and analyzed by qPCR. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, * for P≤0.05). B) Tlk2Δ 9.3.1 cells were treated and analyzed as in 3A. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, * for P≤0.05, ** for P≤0.01). C) U2OS cells were synchronized in G2 and harvested or synchronized in G2 and harvested 16 hours after adriamycin-induced DNA damage. Samples were analyzed by western blot for the indicated proteins. D) U2OS cells were transfected with the indicated siRNA's, synchronized in G2 and damaged with 6 Gy of IR. Cells were harvested 24 hours later and the mitotic index was analyzed by FACS. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, ** for P≤0.01). E) Cells were treated as in 4C. F) U2OS cells were transfected with the indicated siRNA's, arrested in G2 with Adriamycin and induced to recover by addition of caffeine. Mitotic index was analyzed by FACS. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, ** for P≤0.01). G) U2OS cells were synchronized in G2 and harvested 16 hours after adriamycin-induced DNA damage. Samples were analyzed by western blot for the indicated proteins. H) U2TR cells stably expressing Tlk2 siRNA #3-insensitive tetracycline-inducible FLAG-Tlk2-wt were thymidine synchronized, damaged in G2 and harvested 24 hours afterwards. Tetracycline was either absent (off), added from the start of the experiment (early) or for 16 hours after induction of DNA damage (late). I) Cells were treated as in 5G and recovery was induced by addition of caffeine for 8 hours. Mitotic index was analyzed by FACS and normalized to the control. Error bars represent SD of three independent experiments. Error bars represent SD, n=3. Statistical significance was tested using a paired two-tailed t-test (NS for P>0.05, ** for P≤0.01). J) Model of Tlk2/Asf1A-dependent recovery competence. Red circle denotes phosphorylation event at S166, white circles denote histones. See text for further details.
Figure 2Heatmap showing transcriptome profile correlation values of indicated lung tissue samples before and after PAO1 infection. Histogram of selected differentially expressed genes of LL-37+/+ mouse lung versus wild type FVB mouse lung prior to infection. Blue bars indicated genes up-regulated in wild type FVB mouse lungs, red bars indicated genes up-regulated in LL-37+/+ mouse lungs. Enriched gene ontology classes of uninfected (C) and PAO1-infected (D) lungs. Red bar, GO class of up-regulated gene in LL-37+/+ mice. Blue bar, GO class of up-regulated gene in wild type FVB mouse lung. GO terms were ranked by the enrichment P-value. E. Protein-protein interaction network of selected genes with high expression level in PAO1-infected wild-type lung (blue) and PAO1-infected LL-37+/+ lung (red), respectively.
Figure 3Representative auto- (green and violet curves) and cross-correlation (CC, BAX-DRP1, grey curves) curves of DRP1-AF488 and BAX-AF633 measured by FCCS in solution (A) Dash gray line depict raw data and solid lines correspond to data fitting. Representative auto- (green and violet curves) and cross-correlation (CC, BAX-DRP1, grey curves) curves of DRP1-AF488 and BAX-AF633 measured by FCCS in the membrane of GUVs (B). Dash gray line depict raw data and solid lines correspond to data fitting. C) Quantification of %CC between DRP1-AF488 and BAX-AF633 in solution (grey), in the membrane (violet), and in the membrane (beige) in presence of excess unlabeled cBID. Box plots represent the interquartile (outer box), mean (inner box), median (line) and range (whiskers). Levels of significance were determined by paired two-tailed Student´s t-test (* p < 0.05, ** p < 0.01) from n=9 measurements in solution, n=46 individually measured GUVs in the membrane or n=17 GUVs in presence of cBID. D) Effect of DRP1 on BAX-induced LUV permeabilization. BAX was activated by cBID (blue lies), or mild heat (42°C, grey lines). Data are presented as mean ± SD of n=3 individual experiments. Significance was determined at the end-point of the kinetic measurement (180 min) by paired two-tailed Student´s t-test (* p < 0.05, *** p < 0.001). E) Effect of DRP1 on BAX-induced GUV permeabilization. Left: % GUVs permeabilized to Cytochrome c488 (Cyt c, 12 kDa, beige) and allophycocianin (APC, 104 kDa, blue) in the absence or presence of cBID, BAX and DRP1 combined as indicated. Data are presented as mean ± SD of n=4 independent experiments. * p < 0.05 (paired two-tailed Student´s t-test). Right: representative confocal microscopy images showing GUVs (grey) in a solution of Cyt c (green) and APC (magenta). Scale bar 10 µm. Effect of BAX on DRP1 membrane density and DRP1-induced shape alterations of liposomes measured by flow cytometry. F) Representative flow cytometry plots outlining DRP1 (Alexa Fluor 488 signal) binding to LUVs (Rhodamine signal) in the absence or presence of BAX. % DRP1-positive LUVs indicated in green. Effect of BAX on DRP1 membrane density and DRP1-induced shape alterations of liposomes measured by flow cytometry. G) Membrane density of DRP1 (corrected fluorescence units, cFU, left graph) and DRP1-induced membrane tethering (indicated by a shape index > 1, right graph) in LUVs in the absence or presence of different concentrations of BAX. Data are presented as mean ± SD of n=3 independent experiments. * p < 0.05 (paired two-tailed Student´s t-test) vs. DRP1 without BAX.
C/EBPβ confers complete resistance to inhibitory effect of IFN-γ and IL-4 on iTreg generation A, B Flow cytometry of intracellular Foxp3 staining in CD4+ naïve T cells transduced with control retrovirus (MigRI) or retrovirus encoding C/EBPβ and cultured for 2 d under conditions as indicated.Figure 2Flow cytometry of intracellular Foxp3 staining in CD4+ naïve T cells transduced with control retrovirus (MigRI) or retrovirus encoding C/EBPβ and cultured for 2 d under conditions as indicated. Representative experiments are shown in the upper panel and pooled data from 4 (A are shown in the bottom. Dot plots are gated for CD4+GFP+ and numbers indicate percent Foxp3+ cells in the gate. Error bars represent mean ± s.e.m Flow cytometry of intracellular Foxp3 staining in CD4+ naïve T cells transduced with control retrovirus (MigRI) or retrovirus encoding C/EBPβ and cultured for 2 d under conditions as indicated. Representative experiments are shown in the upper panel and pooled data fro ), 3 (B are shown in the bottom. Dot plots are gated for CD4+GFP+ and numbers indicate percent Foxp3+ cells in the gate. Error bars represent mean ± s.e.m Real-time qRT-PCR analysis of FACS-sorted GFP+ cells from CD4+ naïve T cells transduced with control retrovirus (MigRI) or retrovirus encoding C/EBPβ and cultured for 2 d in the conditions as indicated. Data are representative of two independent experiments with consistent results and normalized with β-actin (mean ± s.e.m. of triplicates) Body weight of RAG-2-/- mice after transfer with 5 x 105 CD4+CD45RBhigh cells alone (circles) or with 2 x 105 FACS-sorted CD4+GFP+ cells transduced with control retrovirus (MigRI) (squares) or retrovirus encoding C/EBPβ (triangles) and cultured for 2 d in the presence of TGF-β and culture supernatant. Each time point contains three (circles) or four (squares and triangles) mice in each group. Error bars represent mean ± s.d Hematoxylin and eosin staining of the distal colons of mice (Scale bars, 200μm Histological scores Each symbol represents an individual mouse. Small horizontal lines indicate the mean (error bars, s.e.m) Comparison of the spleen weight Each symbol represents an individual mouse. Small horizontal lines indicate the mean (error bars, s.e.m)
Figure 5Exposure of the catalytic Cys431 is parkin as assessed by reaction with a UbVS probe. The different stages of activation using parkin, parkin:pUb, pParkin:pUb and pParkin:pUb in combination with an isopeptide linked UbcH7-Ub conjugate are indicated above each gel. Following addition of UbVS, samples were taken at the times indicated (0-10 minutes) and visualized by SDS-PAGE.   Relative percentages of pParkin and the pParkin-Ub adduct as a function of time. Intensity percentages were calculated as a function of total intensity of pParkin -Ub, parkin and UbVS/pUb bands. Error bars represent standard deviation from the average for duplicate measurements.  Exposure of the catalytic Cys431 is R0RBR parkin as assessed by reaction with a UbVS probe. The different stages of activation using R0RBR, R0RBR:pUb, R0RBR:pUb:pUbl and R0RBR:pUb:pUbl in combination with an isopeptide linked UbcH7-Ub conjugate are indicated above each gel. Following addition of UbVS, samples were taken at the times indicated (0-60 minutes) and visualized by SDS-PAGE   Relative percentages of R0RBR and the R0RBR-Ub adduct as a function of time. Intensity percentages were calculated as a function of total intensity of the R0RBR-Ub, R0RBR and UbVS/pUb/pUbl bands.
Impact of TMPRSS2 and IFITMs on the kinetics of fusion by S-expressing 293T cells.Figure 3A. 293T-GFP1-10 and -GFP11 cells (1:1 ratio) were co-transfected with S, ACE2, TMPRSS2, IFITM or control plasmids. Cell fusion was quantified by measuring the GFP+ area by high-content imaging after 18h. (B and C) or analyzed over time by video microscopy (D and E). B. Representative images of cell-cell fusion. Scale bar: 100 µm. C. Quantification of GFP+ areas. Results are mean±sd from 5 independent experiments. D. TMPRSS2 accelerates fusion. Cells were monitored by video microscopy and the GFP area was quantified over time. Left panel: one representative experiment. Results are mean±sd from 3 fields per condition. Right panel: Mean±sd from 7 independent experiments (at 12h post transfection). E. Impact of TMPRSS2 and IFITMs on the kinetics of fusion by S-expressing 293T cells. One representative out of three independent experiment is shown.
Figure 5A Schematic drawing of domain architecture and truncations of human G3BP1. B Coomassie blue staining of purified cGAS, full length and truncated G3BP1 recombinant proteins. C cGAS-G3BP1 interaction analysis. Full-length and truncated G3BP1 was pulled-down using anti-Flag M2 beads. The cGAS-G3BP1 interaction was further analyzed with immunoblotting (IB). 2 μg recombinant full-length cGAS and 2 μg each of truncated G3BP1 were used in the assay. D, Time-lapse imaging of DNA-induced LLPS of cGAS, in the presence of full length or truncated G3BP1 (2 μM) n = 3 biological replicates.10 μM cGAS, 100 nM dsDNA were used in the assay Data information: Representative images are shown Scale bars, 10 μm , E Partition coefficient of D was calculated as the total fluorescence intensity of droplets / bulk fluorescence intensity of background (E). n = 3 biological replicates.10 Data information: Error bars, mean with s.d. F cGAMP production assays. Recombinant cGAS (10 μM) and full length or truncated G3BP1 (10 μM each) were incubated, in the presence or absence of dsDNA (200 nM). The produced cGAMP was quantitatively analyzed by LC-MS/MRM. n = 3 technical replicates. Data information: Error bars, mean with s.d.
Sensitivity and dynamics range of pcMNPs-based viral RNA detection.Figure5RT-PCR assays amplifying the N gene in pseudoviral RNA following the Conventional RT-PCR protocol, and (B) corresponding calibration curve. RT-PCR assays amplifying the N gene in pseudoviral RNA following the Direct RT-PCR protocol, and (D) corresponding calibration curve. The red line is the linear regression fit (R2 = 0.998).
Model of HERK1/ANJ involvement in pollen tube reception.Figure 6A Overview of the contact point between the male and female gametophytes at pollen tube reception. B Proposed mechanism(s) of pollen tube reception at a molecular level where HERK1 and ANJ form alternative co-receptors with FER and LRE. Unknown components or interactions are shown in grey. Maternally- or paternally-derived RALFs could act as ligands for the HERK1-LRE-FER/ANJ-LRE-FER heterocomplexes. C Four possible scenarios where kinase activity of HERK1/ANJ are not required for signal transduction during pollen tube reception. Red components indicate proteins active in signal transduction while black proteins act as scaffolds for complex assembly. Each scenario is discussed in more detail in the discussion section.
Membrane structures induced by MERS-CoV infection.Fig 1.(A) Electron micrograph of an area with abundant double-membrane spherules (DMSs). DMVs (asterisks) are interspersed and surrounding the DMS cluster. (B) Slice through a tomogram (left) and corresponding surface-rendered model (right) of a representative area containing the different types of MERS-CoV-induced membrane modifications: DMSs (orange), convoluted membranes (CM, blue) and DMVs (yellow and lilac, outer and inner membranes). The model also highlights ER membranes (green) and a vesicle (silver) containing new virions (pink). (See also S1 Video). (C) Comparison of DMSs and virions (arrowheads in left and right panels, respectively) in enlarged views of tomographic slices from the regions boxed in (B). The DMSs are similar in size but distinct in appearance from newly-formed MERS-CoV particles. (D) Whisker plots of the size distribution of DMSs (n=58), virions (n=28) and DMVs (n=109), as measured from the tomograms. DMSs and virions have a comparable size (median diameter, 80 nm), while the median diameter of the DMVs is 247 nm. (E) Models and tomographic slices through an open (left) and closed (right) DMS. Both types of DMSs are connected with the CM. In open DMSs, both the inner and outer membranes (dark blue and orange, respectively) are continuous with CM. Two ~8-nm apart slices through the reconstruction are shown. For closed DMSs only the outer membrane is connected to CM, while the inner membrane seems to define a closed compartment. (F) Gallery of tomographic slices highlighting membrane connections between different elements of the MERS-CoV RO, and of these with the ER. These include CM-ER (black arrowheads), DMV-ER (white arrowheads), CM-DMV (dark grey arrowheads), and CM-DMS (light grey arrowhead) connections. Scale bars, 250 nm (A, B), and 100 nm (C -F).
Figure 3A. Levels of HY5 transcripts in leaves of reciprocal grafts of phyB1B2 (phyB) and wild-type (WT) tomato plants grown under white light (200 µmol m-2s-1) for 7 d. B. Levels of HY5 transcripts in roots of reciprocal grafts of phyB1B2 (phyB) and wild-type (WT) tomato plant grown under white light (200 µmol m-2s-1) for 7 d. C. Accumulation of HY5 protein in leaves and roots of reciprocal grafts of phyB and WT plants grown under white light (200 µmol m-2s-1) for 7 d. Rubisco and β-Actin were used as loading controls for leaves and roots in the western blot analysis, respectively. The values shown above each lane indicate the relative abundance of the HY5 protein. D. Accumulation of HY5 protein in the roots of WT and phyB plants under high (H, 2.0) or low ratio of (L, 0.5) red (R) to far red (FR) light conditions. β-Actin was used as loading controls in the western blot analysis. The values shown above each lane indicate the relative abundance of the HY5 protein. E. Accumulation of HY5:3HA protein in leaves and roots of reciprocal grafts involving HY5-OE and WT plants grown under white light (200 µmol m-2s-1) for 7 d. Rubisco and β-Actin were used as loading controls for leaves and roots in the western blot analysis, respectively.
An Hsc70 binding site close to the trimerization domain of Hsf1 is necessary for Hsc70 mediated dissociation of Hsf1 from DNA.Figure 4A Hsp70 binding score as predicted by a published algorithm The score value is attributed to the center of the sequence window of 13 residues. Values below -5 are considered to be good Hsp70 binding sites. Small horizontal gray and black lines underneath the prediction curve labeled with HX to the right represent the segments protected from hydrogen exchange. B KD values for the indicated peptides as determined by fluorescence polarization. Peptides N74-Q86-C (NMYGFRKVVHIEQC), P223-H235-C (PKYSRQFSLEHVHC) and A343-R352-C (ASVTALTDARC) represent the most hydrophobic part of HX protected segments 78-98, 229-252, and 347-375, respectively; N200-K208-C (NRILGVKRKC), N200-K208-C_SSS (NRSSGSKRKC), G204-N214-C (GVKRKIPLMLNC), and G204-N214-C_SSS (GVKRKSPSMSNC) represent the two potential Hsc70 binding sites in segment 202-213 in original sequence or with hydrophobic residues replaced by serine; S461-Q471-C (SGKQLVHYTAQC) and Y468-S480-C (YTAQPLFLLDPGSC) represent the two potential Hsc70 binding sites in segment 442-474. C Hsf1(1-408) with a deleted TAD is dissociated from HSE-DNA by Hsc70, DnaJB1 and ATP with similar rates as Hsf1wt. Fluorescence polarization assays containing Alexa Fluor® 488-HSE-DNA bound Hsf1(1-408) trimers and the indicated components. D The HR-B proximal Hsc70 binding site is essential for Hsc70/DnaJB1-mediated dissociation of HSE-DNA bound Hsf1.