EMBO/sd-character-level-ner huggingface dataset:
(B) Fusion and fission time chart for individual mitochondria. Individual mitochondria tagged with mtPA‐GFP were monitored for a period of 1 h and the occurrence of fusion and fission was recorded. Mitochondria in INS1 and COS7 cells spend 77s (±71 s) and 87 s (±78 s), respectively, in the post‐fusion, connected state, and an average of 1434s and 1172 s, respectively, in the solitary, post‐fission state.
(I) Immunoblots depicting levels of PSD 95, GFAP, Synapsin 1 and tubulin in the whole cortical lysate and the synaptoneurosome preparations. Quantification representing the average fold enrichments of PSD 95, Synapsin 1 and GFAP in the synaptoneurosome preparations compared to the whole cortical lysate. Data presented as mean ± SEM with scattered data points. Data points for all the proteins were normalized to their respective whole lysate values. **p<0.05, **p<0.01, n ≥ 7 animals for each group. One-sample t-test.
A, B Schematic diagram (A) and experimental setup (B) of BFP assay to characterize force-dependent dissociation kinetics of NKG2D binding with different ligands.
D Zygotic grk2i283 mutant at 4dpf compared to wild type (N=80). Arrows indicate the position of swim bladder. Scale bar, 1mm
Pulse-chase [35S]methionine radiolabeling of mitochondrial translation products in wild type and MITRAC15-/- cells. Samples were analyzed by SDS-PAGE and digital autoradiography. Signal intensity of ND2 was normalized to the ATP6 signal and the relative ND2 stability was calculated by relative chase ND2 signal/relative pulse ND2 signal (error bars indicate SEM from three biological replicates; *p < 0,05; unpaired t-test).
C) Deletion of endogenous Pvt1 by an inducible Cas9 (iCas9) system can significantly reduce Pvt1 RNA level (quantification from RT-PCR, left panel) and MYC protein level (quantification from immunoblot, right panel) expression. n=3, P<0.01 (Student's t-test). Error bar represents S.D.
(B) UMAP plots depicting the cumulative expression levels of previously published core signature genes for microglia, CAMs, monocytes, and cDC2. CAMs, CNS-associated macrophages; DC, dendritic cell. The scale bars represent color coded sequencing depth-corrected log transformed transcript counts.
A schematic of how FtsZ abundance changes. FtsZ is repressed by the transcriptional factor, PdhR. PdhR is activated by Crp-cAMP. FtsZ is also degraded primarily by the ClpXP protease complex. An approximate FtsZ threshold model poses a basal synthesis rate (α0), a feedrate-dependent synthesis (α1f), and a degradation term (the Michaelis Menten term) to explain changes in FtsZ abundance with and without pulsing. Per the model, FtsZ would deplete via degradation during starvation, be synthesized with glucose pulsing, and engender division when its abundance reaches the threshold concentration
(A) Left: Immunoblot analysis of smooth muscle marker gene expression in control and FRS2 knockdown HASMCs. Blots are representative of four independent experiments. Right: Band intensities of SM -actin, SM22, and SM-calponin were normalized to -tubulin and expressed as a fraction of a control value. Results are expressed as means ± SD (**p<0.01; ***p<0.001 compared to control; unpaired two-tailed Student's t test).
A. The human NDC sequence and the cryo-EM structure of the MT-bound conformation, including the short N-terminal flanking region. Pathogenic mutation sites (Appendix Table S1) are indicated in the sequence with red circles. Side chains of residues representing the mutation sites are depicted in green if they contribute to protein surface (mediate or likely mediate MT binding) or white if they lie in the domain core. MT-binding residues are numbered, and secondary structures are labelled. H, α-helix; S, β-strand.
D: Median RNAseq expression of individual HIFα targets as split by median HIFi-CCS (left) or HIFi-BCS (right). Transcripts up/downregulated by ±1.5-fold are shown in blue or yellow, respectively. Error bars indicate 95% CI of the median. Log2 scale; n= 209 (colon, TCGA) or n= 609 (breast, METABRIC).
IAPV-IRES diagram colored according to secondary structure motifs. Bottom, a closer view of the IAPV-IRES PKI highlighting its sequence, with base pairs indicated as well as the Variable Loop Region (VLR) and stem loop III (SL-III).
d, Localization of beclin 1 and GM130 (a Golgi marker) in HeLa cells stably transduced with empty vector (left panel) or GAPR-1-Myc (middle panel) or transfected with GAPR-1 siRNA (right panel) and treated with peptide (20 μM, 1 h). Scale bar, 20 μm.
A. Volcano plots of differentially expressed genes in pair-wise comparison of 40-day Drosophila treated without ALA administration to 40-day Drosophila treated with 0.5 mM ALA administration. Blue symbols indicate significantly downregulated mass bins (Log2 FC < -0.6 and p < 0.05), red symbols indicate significantly upregulated mass bins (Log2 FC > 0.6 and p < 0.05), and gray symbols indicate mass bins that were not significantly changed.
(F) Representative Western blot (n = 3) for LC3. Chloroquine was added 12 h before cell harvest.
qRT-PCR analysis of the relative Ifnb1 and Ifna4 mRNA expression levels in PICs (n≥5) and PBMCs (n≥4) (B) from WT and Akt2 KO mice Data information: *P < 0.05, **P < 0.01 and ****P < 0.0001; using unpaired t-test Data are representative of three independent experiments Error bars , mean ± SD).
C Quantification of hair follicles (HF) with activated Caspase 3 (aCas3+), apoptotic cells in control (Ctr), K15ΔNLef1 and K15ΔNLef1;Bcl-2EOE mice (n=6 biological replicates; mean ± standard deviation (SD); *** p<0.001, two-way ANOVA test).
F Measurement of blood loss over a 5-minute period after tail transection in mice at 8 weeks of age. Wild-type, n=5; F9Y381S, n=6; F9Y381D, n=13; F9383STOP, n=5.
(E) Western blot and densitometry analyses of tight junction proteins (claudin-1 and occludin) and zonulin in duodenum (n = 6). Data information: Data were representative and were the mean ± SD from three independent experiments. P values were calculated by one-way ANOVA followed by Tukey's post hoc test for multiple comparisons.
C Normalized Bcd concentration profiles for the models considered in b at time=2.5 hours. Inset: same on log scale.
(H and I) Immunostaining assay of MAP2 (green) after SOX1 overexpression in V1-PAKI cells on day 35 of dorsal neural differentiation (H), and quantiﬁcation of MAP2+ cells (I), p=0.0001 (V1-PAKI), p=0.0001 (V1-PAKI+ptSOX1+dox). Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). ***p<0.001 versus Ctrl group ; ###p<0.001 versus -dox group (one-way ANOVA).
A slice through the average structure of the apo-state at a position 22 Å away from the middle slice shown in Fig. 1C. The intra-SR extension is boxed on the density in red.
(a,c) HeLa cells (c) stably expressing FLAG-Parkin and either EGFP-VAP-A or HA-VAP-A were treated with CCCP (30 and 10 μM, respectively) for the indicated times, fixed, permeabilized and subjected to immunofluorescence analysis with antibodies to FKBP38, to HA or to FLAG (M2). The fluorescence of EGFP-VAP-A was also monitored directly. (b,d) Higher-magnification views of the boxed areas in a and c, respectively.
(A) The central channel in the apo-PfFNT protomer viewed from the parasite's membrane plane. The channel, calculated by HOLE (Smart et al, 1996), is indicated by blue dots. The two constriction sites are colored red. Residues forming the constriction sites are in green sticks. Residues that line the rest of the channel are in cyan sticks. (B) Representative figure of the calculated diameters of an apo-PfFNT protomer.
Schematics representing data of all Sgs1 phosphorylation sites detected in a large scale, high coverage, phosphoproteomic dataset (Lanz et al, 2021). Bolded sites indicate those subsequently detected in the IP-MS phospho-mapping experiment in Figure 3C. TIM, Top3 Interacting Motif; HRDC, Helicase and RnaseD C-terminal domain.
(C) 8-oxo-dG (orange) establishes a Hoogsteen base pair with dA (cyan) at the primer terminus. Tyr505 and Arg517 (purple) interact with the minor groove of the base pair. The base pair geometry (C1′ distance and λ angles) is indicated at the bottom of the figure. A simulated annealing Fo-Fc omit density map for the pair is also shown (contoured at 3σ).
(A) S2 cells expressing RDH/CH2064-GFP were treated with the protein synthesis inhibitor cycloheximide (CHX) for the indicated time (h: hours). The level of RDH/CH2064-GFP was determined by western blotting using anti-GFP antibody. Tubulin was used as loading control. (B) Quantification of the relative RDH/CH2064-GFP protein levels in (A). Error bars represent ± SEM.
B Wild-type or Cuedc2-/- mice were subjected to a heart ischemia for 30-minute in vivo, followed by reperfusion for the indicated times. Protein was extracted from the area at risk of left ventricle and subjected to immunoblot analysis.
(A-B) Spinal cord sections from 5-month-old WT and Tmem106b-/- mice were stained with anti- neurofascin, anti- LAMP1 and anti-Cath D antibodies. Accumulation of LAMP1 and CathD positive vacuoles at the distal end of AIS was observed in Tmem106b-/- motor neurons. Representative images from three independent mice were shown. Scale bar = 10 µm. n=3. Data presented as mean ± SEM. Unpaired Student's t test. ****, p<0.0001.
Kaplan-Meier survival curve comparing the survival of patients with EGFR and c-Fos double positive osteosarcomas against patients without co-expression of both proteins. (n=52)
B: Response amplitude for all simulated combinations of mRNA half-life and transcriptional delay. Response amplitude is shown over time (columns) and in respect to input function (rows). For sustained signalling, all primary response genes exceed their half maximum response amplitude. Pulse and transient signalling inputs are only sufficient for immediate-early genes and short-lived delayed early genes. Long-lived mRNAs with half-lives greater 120 minutes require sustained signalling inputs to exceed their half maximum response amplitude. Example parameter sets displayed in (A) are marked with asterisk in (B). Dashed lines indicate cluster borders: IEG: Immediate-early genes, t1/2 ≤ 120min and ∆t ≤ 30min. ILG: Immediate late genes, t1/2 > 120min and ∆t ≤ 30min. DEG: Delayed early genes, ∆t > 30min.
D, E. HEK293T cells were transfected with plasmids encoding MYC-FOXP3, FLAG-USP44 (either wild type USP44, "wt" or the C282S mutant). These cells were subsequently treated with cycloheximide (CHX; 5μg/ml) for the indicated time points before harvested and cell lysis. FOXP3 levels and the relative turnover rate of this factor was determined by immunoblotting analysis with anti-MYC antibodies.
Proposed mechanism for the conformational switch in full-length tetrameric GluN1/GluN2B receptor: inter-dimer rolling in the ABD layer is coupled to entry of the NTD layer in its active state. The positive allosteric modulator spermine, which binds the interface between GluN1 and GluN2B NTD lower lobes, enhances receptor activity by stabilizing the NTD compact form and therefore rolling. Conversely, the negative allosteric modulators zinc and ifenprodil inhibit receptor activity by stabilizing an expanded form of the NTDs (lower lobes further apart) thus preventing rolling. The rolling motion facilitates pore opening by acting on the ABD-TMD connecting linkers
(b,c) The percentage of cells with Atg9 translocation was quantied (c) and the expression of UVRAG and actin was determined by immunoblotting (b). Data represent the means:d:; n D300 cells from three independent experiments; NS, not signicant; P <0:01; P <0:001. Scale bars, 10 m.
(a-h) The migration of HEK293 cells expressing mGPR15, qGPR15, tGPR15, cGPR15, aGPR15, and their mutants induced by ligand C10ORF99. Data information: All data shown are generated from at least three technical replicates. Error bars indicate SD (n=3). ***P-value < 0.001; **P-value < 0.01; *P-value < 0.05 (t-test).
D. smFISH co-detection of k 5 mRNAs and GAPDH in subconfluent motile HUVECs. arrows indicate orientation of RNA localisation; yellow dashed lines outline cell borders; red circles highlight smFISH spots; scale bars = 20 µm
TILs isolated from HER-2-E0771 mammary tumour versus lymphocytes isolated from the contralateral mammary fat pad were analysed for CD4+CD25+FoxP3+ regulatory T cells (Tregs) by flow cytometry.
Death rates of panel B plotted against growth rates of panel A shown as circles in a grey-scale. Squares show data obtained using eight other carbon substrates, also listed in Table EV1. Color circles show data obtained by varying growth rate in a chemostat. The black line shows a linear weighted least square fit to log-transformed data, that takes uncertainty in data points into account (see Methods). Data shown as mean ± (standard deviation) SD. Two or three replicates per condition.
B. HEK293/MycBioID-FAM111A cell lines with no treatment (- Dox), or treated with doxycycline, along with DMSO or 100 μM Z-VAD-FMK for 24 h (total inhibition of PARP cleavage was also observed when 50 μM Z-VAD-FMK was used). Total protein from ~ 105 cells was resolved by SDS-PAGE, and probed in western blots with Myc, PARP, or Tubulin antibodies.
(L and M) Immunostaining assay of GABA (green) in control and V1-PAKI cells on day 35 of ventral neural differentiation (L), and quantiﬁcation of GABA+ cells (M), p=0.0001. Scale bar, 100 μm. Data information: Data are presented as mean ±SEM from three independent experiments (n=3). *p<0.05, **p<0.01, ***p<0.001 (unpaired two-tailed Student's t-test).
d, Immunohistochemistry of liver sections from six-week-old Atg5flox/flox; Mx1-Cre mice at the indicated time points after pIpC injection, using anti-ubiquitin antibodies. Arrowheads indicate ubiquitin-positive inclusion bodies. Scale bar, 25 µm.
Dashed lines indicate differential expression thresholds. Differentially expressed proteins indicated in blue. Most pronounced responding proteins indicated in black and labelled. E. Volcano plots showing differential phosphorylation. Labelling colors as in (B).
(I) Collagen1 or (J) Masson's Trichrome staining was performed on TA or Dp muscles from Ctrl or YY1dKO mice. Scale bar = 100 µm.
Percentage of stem cells in different mitotic phases and the percentage of defective mitotic figures in 72hR anterior blastemas of cct3A RNAi and controls in starved conditions after double immunostaining with anti-tyrosine-tubulin and anti-H3P (****P < 0.0001, ***P < 0.001, *P < 0.05 using two-sided Chi-square test; the number of cells analyzed is displayed in Appendix Fig S2B); n ≥ 5 planarians. Representative images are shown. Nuclei are stained with DAPI. Arrows indicate abnormal organization or number of spindle poles and the yellow arrowhead indicates chromosome lagging. Asymmetrical karyokinesis is observed in b11 and b12.
Confocal images demonstrate overlap of GFP tagged mtON with MitoTrackerTM Red CMXRos stained C. elegans hypodermal mitochondria. Scale bar 10 µm.
(E) In vitro incubation with chemical oxidants does not affect the desuccinylase activity of SIRT5. Flag-tagged SIRT5 was ectopically expressed in HEK293T cells, and then purified by immunoprecipitation with Flag-beads and eluted with Flag peptide. The purified Flag-SIRT5 was treated with increased concentrations of Paraquat or H2O2 at room temperature for 1 hr, and then subjected to the desuccinylase activity assay as described in 'Materials and Methods'. The SIRT5 desuccinylase activity was normalized against its protein level. The results are average ± SD of 3 independent experiments. n.s.: not significant (two-tailed unpaired t-test).
D. Western blot analysis showing expression level of MCT12 and β-actin in HBVPs and BMECs. E. Western blot analysis for siRNA efficiency of MCT12.
C Poly‐caspase activity in THEMIS KD 1G4‐CD8 cells. Cells were stimulated for 24 h with NY‐ESO‐1 pMHC tetramers. Camptothecin was used as a positive control for caspase activation. A FAM‐FLICA detection probe was used to assess poly‐caspase activity by flow cytometry. Data shown are a representative example of three independent experiments.D Quantification of poly‐caspase activity of cells from (C). Data from three independent experiments were used in the analysis. n = 3, means ± SEM are shown; two‐tailed unpaired Student's t‐test, *P 0.05, **P 0.01; ns, not significant.
(E) Immunohistochemistry of sections from occipital cortex of a C9orf72 patient and a healthy control with monoclonal anti-GA and antiserum preincubated with 0.1 mg/ml recombinant GST-(GA)15 or GST. Scale bar indicates 20 μm.
(K) Quantification of the diameter of basal actomyosin rings in the non-activated region (NR, green) and activated region (AR, red) showing increased speed (4.8-fold change) and extent of ring constrictions in the photo-activated region (n= >41 cells). The ring diameter was normalized to the mean value of the first time point. The constriction speed was estimated by the slope of a fitted linear function to the data. (L) Light activation of the cell base resulted in a compaction of the tissue in the activated (AR) compared to the non-activated region (NR). Actomyosin rings were counted and normalized to the analyzed area to score ring density, which increased 1.35 times in the activated region after 5 min of photo-activation, showing that cells were still interconnected at the base and that photo-activation did not affect tissue integrity (N = 3 embryos; nNR: 431, nAR: 302). In each box plot, the central mark, the bottom, and the top edge of each box indicates the median, the 25th and 75th percentile, respectively. Whiskers extent to the most extreme data point
H. p62 and LC3 positive ragged-red fibers (*) in PEO patient (P2), normal diet.I. Muscle fibers showing granular LC3-positivity, PEO patient (P1), after mAD. Immunohistochemistry on frozen sections; bars: 50 µm, except for H, 100 µm.
D. Pyrimidine biosynthetic intermediates accumulate when SHMT-M is disrupted compared to the DiCre parental line (C) following rapamycin/glucosamine treatment (mean ±SEM). Pyrimidine biosynthetic disruption islinked to dihydroorotate dehydrogenase (DHODH) inhibition and blockage of the mitochondrial electron transport chain (mETC). Ubiquinone (Q) is the necessary electron carrier for the mETC.
U2OS cells transfected with siCTL, siDDX5, or siXRN2 were subjected to DRIP-qPCR analysis with anti-IgG, and anti-S9.6 antibodies with or without RNaseH treatment. The average and S.E.M. from 3 independent experiments is shown. Statistical significance was assessed using Student's t-test. *: p < 0.05; **: p < 0.01.
The following experiments were performed in glial shNf-1/shTp53 glial cells serum starved 4 hr before assaying. Cells were expressing either Cas9 alone (control) or Cas9 and sgRNA targeting Atg7 (sgAtg7 #1 or #2). B: Immunofluorescence staining of EGFR following 5 or 15 min stimulation with 20 ng/mL EGF. Scale bar: 20 μm.
B, C. Analysis by real-time PCR Arrays of interleukins, cytokines (B) gene expression in the hypothalamus 6h after an acute icv injection of LPS vs saline in WT mice (n=6 per group). LPS-induced fold up-regulation vs saline condition was calculated using the ΔΔCT method according to the manufacturer's protocol.
A Gene enrichments analysis on differentially expressed genes between sorafenib-sensitive and sorafenib-resistant human liver tumors.
J Cell survival assay of sorafenib-resistant HepG-2 cells with wild type METTL3 overexpression or catalytic mutant METTL3 overexpression after treated with sorafenib for 24h under hypoxia condition (1%O2). Scale bar, 1mm.
C. Effect of Sec31A depletion on TRAPPC2 recruitment to SGs. Cells were mock-treated or KD for Sec31, treated with SA, and then immunostained for TRAPPC2 and eIF3 as indicated. Graphs, quantification of TRAPPC2 at ERES and SGs after SA treatment. Mean ± s.e.m., one representative experiment; n=60-80. ** p<0.001, ****p<0.0001, Student's unpaired two-tailed t-test. Data information; Scale bars, 10 µm.
F Validation of the homo-FRET dimerisation probe. The dimerisation sensitive TMR fluorescence of the labelled FRET dimer (2.5 nM) is de-quenched specifically by equilibration with excess unlabelled dimerisation-competent FICDH363A but not monomeric FICDL258D-H363A. Mean ± SD of three independent experiments.
(A) The effects of GAPDH on degradation of Htt-552. The isolated lysosomes were incubated with 10 µg GAPDH and Htt-552 for 30 min at 37°C. At the end of the incubation, lysosomes were collected by centrifugation and the levels Htt-552 were determined with immunoblotting. Values are the mean±SE of three experiments. **P<0.01, *P<0.05 (compared with Htt-552-18Q without lysosomes); ##P<0.01, #P<0.05 (compared with Htt-552-100Q without lysosomes); $$P<0.01 (compared with Htt-552-18Q without GAPDH); P0.01 (compared with Htt-552-100Q without GAPDH).
D qRT-PCR for mRNA expression of the transcription factors Lef1 and Runx1 in epidermis of ABT-199 treated and control (Ctr) mice at P77 (n=3 biological replicates; mean ± standard error of mean (SEM); ** p<0.01, ns=not significant, two-tailed unpaired Student's t-test).
Bone marrow cells from WT and Akt2 KO mice (CD45.2) were adoptively transferred to lethally irradiated CD45.1 mice and infected with VSV. Survival rates (F left panel), serum IFNβ1 concentrations (F right panel, n=5) were analyzed Bar, 100 μm. Data information: *P < 0.05, **P < 0.01; using a paired t-test or log-rank (Mantel-Cox) test Data are representative of three independent experiments respectively in which the different groups of mice were sacrificed and quantified for indicated experimental purposes
(C) The expression of several core pluripotency markers was determined with qPCR at different time points during reprogramming and normalized against those in MEFs.
A. Isosurface top view of the whole 13-PF MT cylinder and a side view close-up on NN binding site at the vertex of 4 tubulin dimers, where NDC of NN decorates the MT lattice. α-tubulin, white; β-tubulin, grey; NDC, blue. The valley between PFs 1 and 13 represents MT seam, where NN does not bind.
B HA and NP represent the Cal/7/9 wildtype proteins. Chimeric HA (cHA) 1 contains the head regions of H2 HA, cHA2 of H10 HA and cHA3 of H13 HA, while they all contain the Cal/7/9 HA-stalk region. Headless HA (HL) contains a deletion in the HA-head region (dashed line). Modified headless HA (mHL1 and mHL2) contain stabilizing mutations (black boxes) and lack additional internal parts. All constructs were codon-optimized and carry a V5-tag at their C-terminus.
(C) Volcano-plots demonstrating enrichment of transcripts in either the somatic (red) or process (yellow) compartment with representative genes highlighted.
(B) Total lysates from Δapg5 cells with HAAPG10 and/or MycAPG12 on 2μ plasmid were immunoprecipitated with anti‐HA (mAb 16B12) or anti‐Myc (mAb 9E10) antibody. Precipitates were analyzed by Western blotting using anti‐HA or anti‐Myc antibody. Apg12p adduct of Apg10p is indicated by ● and an unidentified complex of 67 kDa by ●●. The positions of cross‐reacting IgG heavy chain (H) and light chain (L) are indicated by arrowheads.
B Cal/7/9-specific serum antibody titers in individual sera at indicated time points. Black lines: individual animals, red lines: mean titer. Statistical significance between pre-immune and immune sera was determined using Friedman test with Dunn's multiple comparison testing (*p<0.05, **p<0.01). The lower table indicates Cal/7/9-specific MN50 and HAI mean titers. Assays were performed in technical duplicates.
B, C The BWM-specific RNAi against myrf-2 improves sarcomere in the worms at day 8 of adulthood. Arrowheads and arrows respectively denote the gaps of myofilaments and the disorganised myofilaments with GFP aggregations. Scale Bar: 10 μm. Mean ± SD. Unpaired t-test, two-tailed. n>=50.
(M) The vemurafenib decreased melanoma cell density. Cell lines have been exposed to Vem (1 or 5 µM, 84h) to define two groups of cell lines (sensitive (blue) and "resistant" (red) cell lines). Normal human melanocytes (NEHM) have been used to evaluate the effect of Vem on normal cells (mean of 3 independent donors).
g, Reduction of percentage autophagic area by 3-methyladenine (3-MA; n = 22 cells).