EMBO/sd-character-level-ner huggingface dataset:
Schematic representation of two potential working alternative possibilities. Red dots show photoactivated tPH-CynA, green dots show not converted tPH-CynA. Left shows that if the biosensor remains associated with the vesicles, a larger proportion of the red signal will appear at the back. Right shows that if the biosensor disassociates from the vesicles, a much smaller amount of the red signal will appear at the back.
(E, F) Maturation of progenitor cells are assessed by staining with BrdU and NeuN. Brain sections were prepared 21 days after BrdU injection Each hippocampal section was 40 μm in thickness, and a total of 24 sections were obtained from one hippocampus. Scale bars:100 μm in the large panel, and 10 μm in the magnified images. Values are shown as mean ± SEM and tested for statistical significance by one-way ANOVA followed by Bonferroni post hoc test. N = 3 animals for each condition, *P< 0.05, **P< 0.01.
J Western blot analysis of proteins extracted from PC3-LN4 cells treated with DMSO or the combination of Pim447 and AZD5363 for 96 h using the specified antibodies.
(A) TAG levels in exoc3(RNAi)-treated planarians vs. gfp(RNAi)-treated controls as determined by UPLC-MS/MS, [n=4 experimental replicates on pools of 25 planarians per group per experiment; data were normally distributed
(c) Blockage of pseudouridylation by deletion of specific pseudouridylase genes. RNAs isolated from wild-type and pseudouridylase-deletion strains (indicated on the top) were used for U2 pseudouridylation assay (CMC modification followed by primer-extension). Primer-extension pauses/stops correspond to ψ sites (indicated on the left and right). Note: The above-background signal of ψ42 in the snr81Δ lane (and to some extent, in the snr81Δ pus7Δ lane) is likely caused by the presence of strong ψ44 band. This is a primer-extension artifact, which often occurs when there is a strong ψ signal in the neighboring position. Alternatively, it is possible that having ψ at position 44 allows for an unidentified enzyme other than snR81 to modify U42 (albeit inefficiently) (Perhaps Pus1, which is responsible for ψ44 formation, can be a bit "processive"). Lanes 1-8 and lanes 9-16 are from two separate gels.
A-B) Western-blot analysis for GAPDH and LC3 of protein lysates obtained from HeLa cells treated with DMSO or 1 µM rapamycin (Rapa) for the indicated time periods (A) (n = 7) or for 5 h with the indicated concentrations (B) (n = 6). One hour before harvesting, 100 nM bafilomycin A1 was added. Upper panels: representative Western blots; lower panels: quantification of the LC3-II/GAPDH ratio.
F. Cumulative survival of mice that received 106cells of TCRβ-rearranged myeloid DN2-derived clones leading to death within 33±4 days after transplantation. Two DN2 clones were transplanted into 5 recipient mice.
H mtm‐3 and epg‐6 mutant L1 larvae have shortened mean and maximum life span in the absence of food. At least 300 animals were scored each day.
Figure 5 - Destabilising Kinesin-8 accumulates behind the stabilising Tea2 kinesin complex to ensure microtubule disassembly at the cell end. The MT stabilising Tea2 complex (Tea2/Tip1/Mal3) binds to MT plus ends containing GTP-β-tubulin (green and yellow subunits) as they grow towards the cell end. The MT destabilising Kinesin-8 (Klp5/Klp6/Mcp1) complex walks along the MT lattice and accumulates behind the Tea2 complex, particularly as the MT dwells at the cell end, but is prevented from accessing the plus end by the presence of Tea2. The Kinesin-8 complex may then either displace the Tea2 complex from the plus end, triggering MT catastrophe, or initiate MT depolymerisation resulting in the loss of the Tea2 complex and the GTP cap. An alternative, but not necessarily exclusive, possibility is that displacement of Tea2 from the MT plus end initiates Kinesin-8 mediated MT disassembly. In the absence of the MT destabilising Klp5/Klp6/Mcp1 complex (second column), MTs dwell for longer at the cell end and the Tea2 complex remains at the plus end during this period. Klp5/Klp6/Mcp1 is therefore essential for regulating timely dissociation of the Tea2 complex from plus ends. In the absence of Tea2 (third column), Kinesin-8 accumulates at, and has unrestricted access to, the plus end resulting in frequent MT catastrophe before reaching the cell end. When both stabilising and destabilising kinesin complexes are absent (fourth column), MTs reach and dwell at the cell end and may undergo catastrophe as a consequence of compressive force encountered at the cell end.  Expanded View Figure Legends
(A, B) Actively dividing cells labelled by BrdU and Ki67 are reduced in the SGZ of DSCR1 mutants compared to that of wild type mice. Brain sections were prepared 1 day after BrdU injection. The white box area is magnified in the lower panels: DAPI (blue), Ki67 (green), and BrdU (red). Arrow heads indicate BrdU and Ki-67 double positive cells in the SGZ.
(E) Viability of wild type, phm8 and pnp1/urh1 strains in oxidative stress. The y axis represents percentage of survived cells calculated by dividing the number of colonies formed after oxidative stress by the number of colonies formed under the same starvation condition but without H2O2 treatment (mean±range of N=2 biological replicates).
A Time-lapse imaging of cGAS-G3BP1 condensates. Data information: Representative images are shown Scale bars, 10 μm 45 μM cGAS-mCherry, 10 μM G3BP1-mEGFP were used in the assays.
(A) Immunoblots of mitochondrial fractions from siRNA‐transfected HEK293T cells±CCCP.
Quantification of different classes of cortical progenitors: apical radial glia cells (aRGs) as Pax6+ NPs in VZ (G), basal intermediate progenitors (IPs) as Tbr2+ cells in SVZ (H) n ≥ 3 brains. Data information: the number of positive cells was quantified in 100µm-width boxes, randomly placed across the LP. 2-way ANOVA (*P<0.05, **P<0.01, ***P<0.001).
Focused miRoot analysis of the PLT1 translatome signal in WT versus hyl1 columella.
G ARChIP‐exo library validation on antagonist‐responsive and agonist‐responsive AR locations referred to (F). The data are the mean of triplicates ± SD.
Western-blot against the hemagglutinin tag within the nascent chain FtsQC40 reveals a cross-linking product of ~80 kDa in presence of nanodisc-reconstituted SecYC282EG and SecYC283EG, presumably assigned to FtsQxSecY adduct. The double band for FtsQC40 likely indicates the incomplete cleavage of the hexa-histidine tag by 3C protease.
(C) Quantification of numbers of GFP-LC3 vesicles in HeLa cells stably expressing GFP-LC3 treated as in (A) and then shifted to starvation media (HBSS) or complete media (Basal) for 2 hr (in the presence of Wm) (mean ± SEM).
Design concept. Bacteria are engineered to exhibit collective survival. Bacteria confined in the microbial swarmbot can maintain a high local density and survive. Cells escaping the swarmbot will have a reduced density due to a larger extra-capsule environment. If their density drops below their survival threshold, they will die, leading to safeguard control.
Sex chromosome recombination was perturbed in 6-month-old Usp26-/Y mice. Immunofluorescence analysis of ; SYCP3 (green), γH2AX (red) (H); SYCP3 (green), ATR (red), p-ATM (pink) (I) was performed in 6-month-old Usp26+/Y and Usp26-/Y spermatocytes. Nuclei were stained with DAPI (blue). The arrows indicate the sex chromosomes.
D, Affinity capture of proteins by OC43p and OC43-SCR bound magnetic beads. Specific reactivity to Atp1a1 and Atp1a2 was detected by protein immunoblotting using specific primary antibodies. OC43p-SCR-coated and uncoated beads (Beads) were used to control non-specific binding. Spinal cords were isolated from male (M) and female (F) rats (n=2/group). Input protein lysates (right side, in duplicates) served as loading controls. Approximate molecular weights (in kDa) are indicated by arrows.
F. Decreased performance on the rotarod test was observed in SOD1G85R/ Sig1R−/−mice. The test was performed at 0-30 rpm with 0.1 rpm/s acceleration every week. Data are shown as mean ± SD. **: p < 0.0001 in SOD1G85R/Sig1R+/+ vs. SOD1G85R/Sig1R−/−, † †: p < 0.0001 in SOD1G85R/Sig1R+/− vs. SOD1G85R/Sig1R−/−. The used animals were the same in the panels B-E. Two-way ANOVA with subsequent post hoc Tukey's test.
H. Representative macroscopic pictures of ear tumors (left panel) and H&amp;amp;E-stained sections of ear acanthopapillomas (upper and middle panel) or an ear acanthopapilloma with trichoepitheliomatous differentiation (lower panel). Boxed areas are shown at higher magnification in subsequent pictures to the right in each horizontal picture panel. E: epidermis; D: dermis; C: cartilage. Scale bars: 200μm (left panel), 100μm (middle panel) or 50μm (right panel).
f, g, Immunoblot of silenced MODE-K cells (f) and primary intestinal epithelial cell scrapings (g) for the PERK-eIF2α branch (n = 3).
Relative expression of SCC marker genes KRT5, 14 and 19 in A-431 cells stably transduced with constitutive shRNA-non-targeting control (NTC), two independent shRNA-ΔNp63, two independent shRNA-USP28 or ΔNp63 in shRNA-USP28#1, normalised to ACTIN. Quantitative graph is represented as mean ± SD of three experiments (n=3).
CD86 MFI and percentages of cytokine-producing cells within pDC of each indicated mouse strain. Black, C57BL6 green, Tlr9-/- and pale green, Tlr7-/-. In (K-L) indicated mice were treated with IC (square) or blocking α-IFNAR1 mAbs (triangle). Data depicted (mean±SEM) are from 2 pooled independent experiments each with 2-3 mice per group.
(E-F) Quantification of 3H-cholesterol delivery to MAM (E) or bulk ER (F) after the indicated times. Control and BI-treated or untreated PS-DKO cells incubated with 2.5 µCi/mL 3H-cholesterol for the indicated times, before subcellular fractionation (Western blot of isolated MAM fractions shown in Fig. EV1F). Cholesterol delivery to MAM calculated by quantification of radioactivity levels in the isolated fractions. Two-way repeated measures ANOVA (Time, Group)( n=3 independent experiments; * p< 0.05)
(K) Proliferation (CFSE dilution) of OTII CD4 cells in co-cultures with anti-Igκ-OVA pulsed B cells; and quantification from 6-8 mice. Data show mean ± SEM.
Analysis of correlation between Sel1L-Hrd1 ERAD and Crebh-Fgf21 during growth Quantitation of levels of Sel1L/Hrd1/Crebh proteins and Fgf21 mRNA with the livers from Sel1Lf/f and Sel1LAlb mice at 3, 9 and 24 weeks of age.
B 3-D reconstructions of PI-stained cell wall (red) and BCECF-stained vacuole (green) of late meristematic cells. Boxplot depicts vacuolar occupancy of the cell. Seedlings were treated with DMSO (n=16) or 50 µM EGCG (n=15) for 22 h on solid medium. Student´s t-test (**p < 0.01). Data information: Boxplots: Box limits represent 25th and 75th percentile, horizontal line represents median. Whiskers display min. to max. values.
Transcriptional downregulation of ISRE/IRF genes in the intestinal epithelium by zinc part 1. RNA-seq experiment of GRWT and GRDim mice which received normal drinking water or drinking water containing 25mM ZnSO4 for 1 week. Ileum was sampled and RNA-seq performed (N=5-6 per group). Genes downregulated by zinc compared to water control animals (LFC<0.8 and p<0.05) were considered. (C) Heat map of a selection of the 48 genes of Fig 3B.
C, E, Control and degron ORP2 cells were co-plated, and after 1 day in 5 % LPDS, treated with 50 μg/ml LDL and IAA for the indicated times. Asterisk indicates an ORP2-depleted cell. Double labeling of intracellular D4H and Lamp1 (C) or intracellular D4H and internalized integrin β1 (E). Images were acquired by confocal microscopy. Red box indicates a peripheral region toward the leading edge in the control cell, and blue box a corresponding region in the ORP2-depleted cell.
Mice were pre-treated with pemafibrate (1mg/kg) or vehicle (0,9% NaCl) for 1 week before being subjected to CLP. Apoptosis in liver paraffin-fixated sections 24h after sepsis, measured with TUNEL staining and depicted as % of PI positive cells/µm² tissue area. P-values were calculated with 2-way ANOVA tests. n = 6-7/group, combined data of 2 independent experiments.
(B) Proliferation assay of Stat3+/+ and Stat3-/- cells cultured in 2i. Cells were seeded and treated for 48 hours with LIF and rotenone (orange bars), a Complex I inhibitor, as indicated. Scores were normalized to Stat3+/+ cells treated with LIF and DMSO. Proliferation was enhanced by LIF treatment in Stat3+/+ cells and reduced by rotenone treatment. Stat3-/- cells resulted more sensitive to rotenone treatment. Mean and s.e.m. of at least 2 independent experiments is shown. Unpaired t-test: * P<0.05 *** P<0.001. n.s. :non significant. See also Appendix Figure S4A.
G, H Heatmaps depicting top 40 differentially expressed genes (G, row scaled log normalized read counts) or transcription factors (H, Library size normalized log2 transformed read counts; from DIE and CTX GM astrocytes. Transcription factors were identified according to the content of AnimalTFDB database (http://www.bioguo.org/AnimalTFDB/).
(F) Co-stimulation of monocytes by LPS plus GM3 species or precursor GSL species. TNF-α, IL-6, and IL-12/23 production were shown in heat maps.
(B) Retinal flat mounts of P17 OIR mice injected with PBS, COCO or Flt1Fc are stained with IB4. Red areas highlight vascular tufts.
(D) Analysis of Atg36 localisation in pex3Δ cells expressing PEX3, pex3‐177 and pex3‐1. The mother cells of pex3‐1 are devoid of peroxisomes (black arrowhead).
H Left panel, concise representation of the mitochondrial reactions mediated by MAOs and ALDHs from a monoamine (R-NH2), to an aldehyde (R-CHO), to the four identified metabolites (R-COOH). The main monoamine origin of each metabolite is indicated in parentheses. Right panel, detail of the histamine metabolism pathway, with enzymes or enzymatic activities marked in red: ALDH, diamine oxidase (DAO), histidine decarboxylase (HDC), histamine N-methyltransferase (HMT), imidazole acetic acid-phosphoribosyl transferase (IPRT), and MAO-B.
(B) Schematic drawing of the truncated Hel2 mutant proteins. Activities in RQC or NGD induced by the R(CGN)12 sequence are indicated.
(U,V) EM sections of P28 WT and HET ONs illustrating the expanded astrocytic processes (surrounded by red dotted lines) among myelinated fibers of P28 ONs. Scale bars: (U,V) (4µm).
Lysates from (H) T47D, BT20, and HA-FGFR2b-transfected BT549 stimulated or not with FGF7, FGF10, EGF, and TGFα for 40 min.;
(E) Track length of single EGFP-positive clones derived from U2OS (EGFP-BIR-5085) cells after Cas9/sgRNA-5085 (n=47) or Cas9n/sgRNA-5085 (n=39) expression was analyzed by sequencing of the PCR products from genomic DNA covering the repair junctions.
The upper schematic illustrates the stage-specific supplementation of splicing inhibitor PLB and on day 8 CD43+ HSPCs were examined by flow cytometry. The bottom bar graph showing the normalized frequency of CD43+ cells to DMSO control under distinct PLB treatment windows. P-values were calculated by one-way followed by Dunnett's test.
C - Same as in (A) except that C. trachomatis serovar L2 (left) or D (right) were grown in primary cells isolated from fallopian tubes. For serovar D, IFU were determined 48 hpi. The mean ± SD of four to five independent experiments are shown. P-values of Student's paired t-test are indicated when <0.05.
F. The relative enrichments of RNAs coimmunopurified with WT Yb and ∆Hel-C. Bars and error bars represent means ± SEM values of three independent experiments. In addition to tj, three genic piRNA sources that were characterized in previous studies (dm/Myc [59], c-Fos/kay [60], and CG9257 [34]) are also shown. rp49 was used as a negative control. p value was calculated by t-test. ***: p < 0.001.
(f) Flow cytometry of CD8+ T cells in the peripheral blood of mice at day 15 after infection as in a (numbers in plots as in c, left).
d, e, LDH release and IL-1β secretion from primed BMDMs infected with SPI-1-expressing logarithmic phase S. typhimurium, treated with monosodium urate, alum and nigericin or transfected with poly(dA:dT) and LPS.
B: Recombinant MSP domains pulled down with STARD3 FFAT peptides (unphosphorylated, mono-phosphorylated on S209 or S213, bi-phosphorylated on S209 and S213, or tri-phosphorylated on S203, S209 and S213.and control peptides were revealed by Coomassie blue staining. The recombinant proteins subjected to the assay are shown in the input fraction.
H Mouse splenocytes of Usp33+/+ or Usp33-/- mice were infected with VSV (MOI=1.0, 24 hrs) immediately after addition of NaCl (+34 mM). VSV-G protein levels were analyzed by Western blot. Data information: Data are representative of at least two biological replicates
quantification of polyGln proteins expressed in transfected HEK293T cells with interrupted or pure polyGln repeats; EV: empty vector; n=3 transfections, ** p<0.01, *** p<0.001, unpaired t test, mean ± SD.
E) Two shcircFNTA plasmids using PLKO.1 vector were transfected into UMUC3 cells. The knock down efficacy was measured by qRT-PCR.
Brown preadipocytes were induced to differentiation with or without 1mM asparagine. Rapamycin (75nM) was added to cells for 48h. Then western blot detected protein expression on day 6.
(A1) Atg30 sequences from aa 68-122 of wild‐type (Atg30), the S71A mutant (Atg30S71A) and two different deletions of the sequence between the AIM and phosphosite required for Atg11 binding in Atg30 (Atg30WDILSSS and Atg30WSILSSS).
G) Aggregate profile showing the mean RNA-seq read coverage observed at and around all motif-associated TSSs identified in this study. The calculated SEM is also shown. The aggregate profile was centered on the TSSs coordinates (relative position 0 bp), indicated by a gray dashed line.
(J) Silencing of ABCA12 in MIN6 cells as assessed by Western blot of ABCA12 immuno-precipitate (top panel) or confocal microscopy in cells transfected with Dy547-siRNAABCA12 (lower panel, scale bar = 10μm).
(C) No ISG20 protein expression in ISG20-/- Sw.71 cells after IFNβ treatment. Sw.71 and ISG20-/- Sw.71 cells were treated with 30 ng/ml IFNβ for 24 h, and proteins were collected for western blot analysis. β-actin served as a loading control for western blot.
D Western blot results of HRH1, SLC22A3, and loading control from Tsc2-deficient and wild-type MEFs exposed to DMSO or treated with 20 nM everolimus for 16 hours in DMEM 10% or 0.5% FBS (independent experiments n = 2). The expression levels are indicated by the ratio of the corresponding signal relative to loading control and basal setting
Karyotypic analysis of later passage, control and ICL of a replicate (#1) of Ch12 (A). All chromosomes are shown for 20 metaphases. Target chromosomes are boxed in red.
D, E Distant metastasis-free survival (D, n = 232) and overall survival (E, n = 241) plots generated using the Kaplan-Meier Plotter based on the mean expression using the signal intensity of the NFIB (213029_at) combined with the ERO1A (218498_s_at) probes. The cut-off was automatically set to split patients into two groups (median), high and low. The plots were generated using the signal intensity of the different probes in Affymetrix microarray gene expression data from TNBC patients of The Cancer Genome Atlas. Number of patients (n) and P values (two tailed log-rank test) are presented in the panels.
Combined median fold-change in protein (B) levels between NUP58 mutant clones and WT cells (calculated using n=4 RNA-seq and n=3 mass spectrometry datasets). Data were visualized using Cytoscape. White: comparable average expression to WT; red: upregulated relative to WT; blue: downregulated relative to WT. Nodes belonging to the same subcomplex are grouped; edges represent physical interactions
(a) Dynamics of replication factories tagged with EGFP (NSP5-EGFP) and mCherry (NSP2-mCherry) visualized in MA104-NSP5-EGFP and MA104-NSP2-mCherry rotavirus-infected cell lines. Live-cell confocal images (4-16 min) acquired after 4 hours post infection (HPI). Scale bars, 5 µm.
In vitro differentiation to mature ookinete of the complemented parasites. Values are means ± SEM (n=4 replicates), two-tailed t test, ***, P<0.001, ns: not significant.
a) VEP analysis. Ratio between contralateral and ipsilateral eye responses (C/I ratio ± SEM) in animals treated with saline and not deprived (sal no MD), with scrambled LNA and MD (scr MD), with amiR-29a LNA and MD (amiR-29a MD). N=6/7; one-way ANOVA, p=0.0003; post hoc Tukey's test: sal noMD vs scr+MD, ns; sal noMD vs amiR-29a+MD, p=0.0002; scr+MD vs amiR-29a+MD, p=0.0169.
Schematic of ORP3 structure. ORP3 contains an N-terminal pleckstrin homology (PH) domain that interacts with phospholipids, an FFAT motif that specifically interacts with VAP-A/B, and a highly conserved C-terminal OSBP-homology domain (OHD).
C) GO terms enrichment analysis for each cluster. The x-axis is the GO term enrichment, the color gradient (black to light blue) indicates the p-value, the number of genes and the GO term category (CC: cellular compound, BP: biological process, MF: molecular function) are indicated between brackets.
C) Cell line characterization of FLAG/HA-tagged PALB2 localization 2 hours following exposure to 15 Gy of IR. Z-stack max intensity image projection and background subtraction was done using ImageJ/Fiji. Scale bar = 5μm.
(B) Quantification of average histone acetylation signal, normalized to loading control. N≥3. Error bars represent SEM. Significant differences, calculated with T-test, between treated and mock conditions are indicated with * (p<0.1), ** (p<0.05) and *** (p<0.01)
Immunoblot analysis of FLAG:AGO1 IPed in each root-tip layer. Scale bars: 50μM, NT: Non-transformed. CB: Coomassie blue.
E-F. Latency to fall during daily training in accelerating rotarod test (left panel, averaged across 3 trials per day) and average over 3 consecutive days (right panel) recorded in control (open circles), cuprizone- (filled black circles) and D-Asp- treated (filled red triangles) mice at 3 weeks (E), and 5 weeks (F) of cuprizone feeding The values represent the means ± S.E.M (n=8 mice for each group) Level of significance was determined by usin left panels (daily training), for each day (d) one-way ANOV P<0.0001 (E, 3d), P=0.0082 (F, 3d followed by Bonferroni post hoc test, #P<0.05 versus cpz at day 1, §P<0.05 versus cpz at day 2, *P<0.05 versus cpz at day 3 right panels (average): one-way ANOV ), P=0.0002 (E), P<0.0001 (F) followed by Bonferroni post hoc test *P<0.05 versus control; ^P<0.05 versus cpz or vehicle (veh)
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).
(D) Filter trap assay probed with anti-FLAG, anti-myc or anti-HA antibodies reveal abundant DPR production. (E) Relative expression level of poly-GA, poly-GP and poly-GR normalized to GR. n=3 experiments, ANOVA, Tukey.
(C) Co-immunoprecipitation using BmN4 cells transfected with the Flag-tagged DEAD-box helicases identified by shotgun proteomics. The Flag-tagged proteins and Ago3 were detected by western blotting. Full-length Flag-tagged proteins are indicated with red asterisks. h.c.: heavy chain.
B Schematic organization of HCoV-OC43 coronavirus ORF1ab polyprotein. Triangles indicate the canonical cleavage sites. Amino acid sequences alignment of homologous MBP84-104 and OC43p plotted using Clustal Omega.
The cells specified below were loaded into the upper chamber of a Transwell migration device without (no) or with the specified chemokines in the lower chamber. The percentage of cells that migrated to the bottom chamber after 2 h (T cells) or 4 h (B cells) is shown. A Chemotaxis of naïve CD4+ T cells from WT and Arghap45−/− mice in response to CCL19, CCL21 and CXCL12. B Chemotaxis of naïve CD8+ T cells from WT and Arghap45−/− mice in response to CCL19, CCL21 and CXCL12. C Chemotaxis of naïve B cells from WT and Arghap45−/− mice in response to CCL19