EMBO/sd-character-level-ner huggingface dataset:
E HDR donor design for correction of Y381D and representative Illumina sequencing reads (rn) in DNA treated HB mice. Red text indicates the correction of mutation, whereas blue text indicates the synonymous mutations.
The genomic structure of mouse Clrn2 (ENSMUST00000053250), and domains of the encoded tetraspan-like glycoprotein (232 amino acids). Black filled boxes represent untranslated region of Clrn2. The positions of the transmembrane (TM) domains (blue) and the structure of Clrn2clarinet (C) and Clrn2del629 (D) alleles are indicated. The clarinet mutation, Clrn2clarinet, (c.12G>A) is predicted to lead to a premature stop codon at position 4 (p.Trp4*) (C), whereas the Clrn2del629 allele consists of a CRISPR/Cas9-mediated 629 nucleotide deletion encompassing exon 2, leading to splicing of exon 1 to exon 3, which if translated would produce a protein lacking 2 (TM2 and TM3) of the 4 transmembrane domains (D).
B) VEGF neutralizing antibody (B20) failed to suppress BCE cell growth induced by LN-229 CM, n=3. Data information: Bars and error bars represent mean ± SD. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test. ns, not statistically significant.
D. Overall structure of PCM1 and the Plk4-mediated phosphorylation site. The conserved serine residue that is phosphorylated in a Plk4-dependent manner is indicated in red.
(J) Bisulfite sequencing analysis of demethylation of Oct4 and Nanog promoters in D-CiPSCs or canonical CiPSCs. Filled and empty squares represent methylated and unmethylated CpGs, respectively.
F. Dot blot of Hsp70 isoform overexpression effect on extracellular tau release in HEK293T cells. Intracellular protein levels are shown with representative Western blot. HSPA variants were detected with V5 antibody. Data are mean ± SEM, n=3 p<0.01 one-way analysis of variance with Tukey's multiple comparison post-hoc analysis.
Histological analysis of colon tumors was shown by hematoxylin and eosin (HE) staining. Tumors were microscopically analyzed and classified as low or high grade. Histological score was assessed by a pathologist. Scale bars, 25 µm.
(a) Changes in groups (carbohydrates, amino acids and fatty acids) of storage metabolites measured in circulating haemolymph with progressing wasting, shown as log2 changes measured by LC-MS and calculated per larvae relative to RasV12; ctrl at day 6.
(N) Genomic snapshots of two of the above identified mitochondrial genes (Tomm40I and Ndufa13) that are bound by YY1 in their TSS (ChIPseq tracks) and up-regulated by YY1 deletion (RNAseq tracks).
E. Schematic protein structure of STIM1 displaying functional motives. Domain A (red) is located 8 amino acids downstream of the inhibitory domain (ID, yellow) after aa 491.
(a) Reaction scheme for Sld3/7/Cdc45 recruitment experiments. DNA substrate was bound to beads and reaction mixtures were removed after each step.
E Protein level of LC3 I/II in HepG-2 and sorafenib-resistant HepG-2 cells under hypoxia condition for 48h.
C, Summary bar graph of the control neurons (corresponds to the traces shown in panel A). Average Ca2+ response (t=20-30s) following stimulation for terminals occupied by a mitochondrion (ΔF/F0 = 3.5 0.4) and unoccupied terminals (ΔF/F0 = 4.9 0.5, n=15 neurons, 96 terminals, ***p<0.001, paired t-test). D, Summary bar graph of the Ru360-treated neurons (corresponds to the traces shown in panel B). Average Ca2+ response (t=20-30s) following stimulation for terminals occupied by a mitochondrion (ΔF/F0 = 4.1 0.5) and unoccupied terminals (ΔF/F0 = 3.8 0.9, n=13 neurons, 79 terminals, p=0.53, paired t-test). Experiments performed in P0 rat hippocampal neuronal cultures at DIV 10-12. Error bars represent SEM.
E) Top canonical pathways discovered by Ingenuity pathway analysis (IPA). Corresponding associated transcripts in acute antiviral and cell signaling canonical pathways are presented as a heatmap showing the Log2 fold change.
A. Western blot analysis of Rho-GTP pull-down assay in MDA-MB-231 and MCF7 cell lines transiently transfected either with control or Flag-RASSF1C plasmid.
F Neutralization of SARS-CoV-2 by the thermostable Re5D06 variants R15 and R28 at the indicated concentrations. The neutralization experiment was performed
C. Despite the complexity of the sample we were able to identify the four states of the 26S proteasome showing the flexibility of the AAA-ATPase dependent heterohexameric ring.
Western blot results showing the levels of CPEB1 in WT and Cnot6l-/- oocytes at the indicated time points after meiotic resumption. Total proteins from 50 (A oocytes are loaded in each lane. DDB1 (A is blotted as a loading control. Experiments were performed three times with reproducible results; a representative result is shown
eATP levels measured from culture medium collected from mock treated and S. indica colonized Arabidopsis seedlings at 3, 5, 7 and 10 dpi. Error bars represent ±SE of the mean from three independent biological replicates. RLU: relative light units. Asterisks indicate significance at p< 0.05 (*), 0.01 (**) analyzed by Student's t-test.
1205Lu cells were exposed, or not, to adipocyte EV from ND or HFD mice with, or without, Lalistat 2 (Lal). Cell motility was then tracked by video microscopy (n=40 cells per group).
Schematic presentation of SUD, Paip1, and PABP. Interactions between SUD and Paip1, as well as PAPB and Paip1 are indicated by red and black lines, respectively. PAM: PABP-binding motif; Paip1M: the middle domain of Paip1; RRM: RNA-recognition motif; PABC: the C-terminal domain of PABP.
PCNA and cleaved Caspase 3 IHC staining and quantification shown as % positive cells (for PCNA) and as positive cells per mm² (for cleaved Caspase 3) in OS from H2-c-fosLTR/Egfrwt (n=6) and H2-c-fosLTR/Egfr∆Ob (n=5) mice. Scale bars: 100µm
(B) UMAP representation of 828 individual microglial cells from brain parenchyma derived from SPF (green dots) and GF (yellow dots).
(A) MCF10A-eGFP-LC3 cells were transfected with indicated siRNAs for 48 h and analysed for the indicated mRNAs (top) and proteins (bottom by RT-PCR and immunoblotting, respectively. Similar results were obtained in three independent experiments.
ITC result of Mac1−2 interacting with Paip1M. The experimental results are: N = 1.14 ± 0.02; Kd = 18.6 ± 2.5 μM; ΔH = -3730 ± 100 cal/mol; ΔS = 9.14 cal/mol/K.
D Chromatograms reveal a homozygous T-to-G substitution (black boxes and arrowheads) in the four affected family members, while a heterozygous G/T in the healthy sibling.
H) Violin and boxplots showing the distribution of end-point solubilities across 11 aggregating cores, grouped by GK. The dotted line indicates a concentration of µM, corresponding to completely insoluble peptides.
(B) Subcellular localization of BET1 in control and patient fibroblasts by indirect immunofluorescent confocal microscopy. Representative immunofluorescence images of BET1 (red) and cis-Golgi marker GM130 (green). Scale bar: 20µm.Colocalization of BET1 with GM130 was determined using Pearson's correlation coefficient (PCC) measured per cell (right panel; C1: n=63, C2: n=50, C3: n=49 and P2: n=33) (***=p≤0.001, one-way ANOVA was followed by Tukey's post-hoc test). Means are shown ± SEM. (C) Representative immunofluorescence images of BET1 (red) and ER marker PDI (green). Scale bar: 20 µm. Right panel shows PCCs for BET1 versus PDI (C1: n=61, C2: n=42, C3: n=59 and P2: n=32 of two biological replicates). (***=p≤0.001, one-way ANOVA was followed by Tukey's post-hoc test). Means are shown ± SEM.
(A and B) Immunostaining image showing Cvt vesicles (marked with arrows in A) in the cytosol. Arrowhead and double arrowheads show the inner and outer membrane of Cvt vesicle, respectively.
MTT assay was performed to assess cell viability 24 hours post treatment. Results are normalized relative to untreated controls and presented as survival rate percentage. The indicated mean and SE for the results are determined from three biological replicates (n=3) and technical duplicates. A JurkatTat cells were treated with the indicated concentrations of the PH compounds.
a, Time lapse analysis of Atg18 added to liposomes. 10 µL of 10 µM purified recombinant Atg18wt was added to 100 µL buffer containing GUVs with 5% PI3P and 1% PI(3,5) P2. The sample was imaged on a spinning disc confocal microscope. Most of the tubules underwent scission into small vesicles (See movie EV6). Scale bar 5 µm. Areas in boxes 1 and 2 of c are shown at higher magnification in b and c. Scale bars: 2.5 µm.
(b) Chromatin immunoprecipitation using α-FLAG antibody was performed to confirm the pull-down of Sα chromatin from the Sα-engineered (FNLDD-Sα-LexA) CH12F3-2A cells. The a, b, and c bars indicate the primers used for ChIP-qPCR as shown in Fig. 1a (n=3; mean + sd; two tailed unpaired Student's t-test).
H. Murine naïve CD4 T cells (CD62L+/CD25-/CD4+) from WT and USP44-/- mice (n=2-3/group/experiment) were FACS purified and activated in vitro for four days by CD3/CD28 cross-linking antibodies (1ug and 4ug/ml, respectively) in the presence of 100 U/ml IL-2 and the indicated dose of TGF-β. Down-regulation of FOXP3 was observed in USP44-/- mice by intracellular immunostaining and flow cytometry.
F. Schematic representation of the GM-CSF/IL-6-induced mouse bone marrow monocyte myeloid-derived suppressor cell (MDSC) differentiation assay (n = 3).
Western blot analysis of cell lysates from the citral-treated HSCs in (A). α-tubulin was used as a loading control. The quantitative densitometric data are expressed as the percentage of untreated control and represent the means (SD) for three independent experiments. **P-value = 0.002, paired t-test (compared to control).
Split violin plots of piRNA expression fold change between AcGFP (control) and piRNA factor(s) overexpressed libraries. Overexpression of Siwi-D670A, BmVasa-E339Q and both mutants increase non-TE-derived piRNA (red, 626 genes) while TE-derived piRNA (blue, 818 genes) does not change. Bonferroni-corrected P-values and the effect sizes (r) were calculated by Asymptotic Wilcoxon rank sum test.
A CUEDC2 ablation reduced I/R injury, which was induced by 30 minutes of ischemia followed by 24 hours reperfusion. AAR, area at risk; LV, left ventricular area, IRI, area of I/R injury. The ratios of AAR to LV, IRI to AAR and IRI to LV are shown. * p < 0.0001 compared with WT, n = 15 mice per group. (top panel) Representative cross-sectional slices derived from the hearts stained by TTC. Area of I/R injury is indicated in light pink.
C) Average composite plots of mono-nucleosomal MSL2 ChIP-seq (Chromatin) centered at PionX (left) or HAS (right) in early and late mixed-sex embryos.
A) Alignment of sequences of all human α- and β‑tubulin isotypes. Only the C-terminal tail region of the tubulins are shown. Isotypes with identical amino acid sequence in these regions are pooled. A large number of glutamate residues in the C-terminal tails would, if modified by glutamylation, be detectable with GT335 (yellow), which requires one additional acidic amino acid residue after the modification site (Wolff et al, 1992). By contrast, the GEF motif (red/purple), which is the main glutamylation site in β2‑tubulin (TUBB2) in the brain (Rüdiger et al, 1992), is present only in a few β‑tubulin isotypes, but not in α-tubulin.
(C) Representative images of LGR5 ISH in human organoids treated with DMSO or TCDD. Scale bar 50 µm.
U2OS cells transfected with siCTL or siPRMT5 were subjected to DRIP-qPCR analysis. The average and S.E.M. from 3 independent experiments is shown. Statistical significance was assessed using Student's t-test. *: p < 0.05; and **: p < 0.01.
G Quantification of TOM20−negative structures that stained positively for the indicated cargo in U2OS:GFP (GFP) and U2OS:GFP−parkin (GFP−parkin) cells, transfected with siRNA targeting Drp1, treated with antimycin A (anti A); both the total number (white bars) and the number colocalizing with GFP−parkin (gray bars) are indicated. Error bars represent the mean ± s.e.m. P−values are given first for GFP−/GFP−parkin−positive vesicles, then for total vesicle number (n = 24-59 cells in two experiments; ns, not significant; ***P < 0.001).
E) The panel shows the lack of induction of bona fide WNT targets in miR-over expressing cells from panel C compared with EV control. UT indicates samples untreated with WNT3.
(E) UBA pull-down of ubiquitinated proteins following antimycin A and oligomycin (AO) treatment of BAX/BAK-deficient HeLa cells ectopically expressing HA-Parkin and BAX for 3 h. Representative immunoblot from two independent experiments.
(I) Frequency of donor derived cells (septin 7fl/fl or septin 7∆/∆) in peripheral blood 8,16 and 21 weeks post transplantation (n=12 per group, error bars indicate mean±SD, ****P<0.0001, Two-way ANOVA analysis).
B, C PAS-stained lung sections of Rag2−/− mice were scanned and inflammation quantified by pixel intensity threshold analysis in ImageJ. FK506-treated animals had increased inflammation at day 2 p.i. compared to control. P = 0.0126 (using Student's t-test), n = 3-5 per group. (C) Close-up of an infectious focus showing increased inflammation and fungal growth in the FK506-treated group. Scale bar: 400 μm.
G. Superimposition of Kap114p (gray) with cargo-bound Cse1p (light orange; PDB code: 1WA5). The HEAT8 hairpin and HEAT19 loop of Kap114p are colored blue and light green, respectively.
(D) Conditioned media experiments were performed on HDMB03 MB cell line. Phosphorylation of Smad2 (P-Smad2) was analyzed by immunoblot upon treatment with either non-conditioned media (NCM), media conditioned with HDMB03 cells (CM-HDMB03) or media conditioned on PDX4 cells (CM-PDX4). Pre-incubation with blocking antibody against ActivinB (Ab α-ActB) or with vehicle was performed before HDMB03 cell-line treatment as indicated. lower panels represent the relative quantification of P-Smad2 normalized to β-actin. The p-values were determined by unpaired t-test. *p < 0.05, **p < 0.01, ***p < 0.001. Bars represent the mean ± SD. Number of replicates is n≥3.
(B) Expression of INHBB in Group 3 MB cell lines and PDXs relative to HDMB03 (set at 1) by RT-qPCR. Bars represent the mean ± SD. Number of replicates is n≥3.
H Immunoassay of IRF3, AKT2, LaminB1 and GAPDH in the nuclear and cytoplasmic fractions from the WT and Akt2 KO PEMs after VSV treatment for 6 hours. Tubulin and LaminB1 were used as cytoplasmic and nucleic protein loading control respectively. Data information: * Data are representative of two or three independent biological replicates
A) Representative cytometry plots of CD11b+ populations present in the cortex of CX3CR1GFP/+ or CX3CR1GFP/+;Sfrp1-/- mice 3 days after saline or LPS intraventricular infusion. Gating was set for isolating the following myeloid cell populations: CD11b+;CD45lo;GFP+ surveying microglia, CD11b+;CD45+;GFP+ activated microglia and CD11b+;CD45+;GFP- infiltrated monocytes.
Abundance changes of proteasome proteins and their transcripts during aging. Members of the 19S and 20S complex are displayed separately and changes are shown for both the age comparisons as box plots. Transcripts are displayed as light blue and proteins as dark blue boxes. Changes of individual proteins are displayed as dots, orange dots represent significant cases (adj. p < 0.05, n=4 per age group for proteome and n=5 per age group for transcriptome). In boxplots, the horizontal line represents the median, the bottom and top of the box the 25th and 75th percentile, respectively, and the whiskers extend 1.5 folds the interquartile range.
C. Quantification of RAB13 Puro-PLA punctae normalised to protrusion area (n≥40 protrusions; *P<0.05, ****P<0.0001; Kruskal-Wallis test with Dunn's correction).
(e) Representative transmission electron microscopy images of well-fed and 6 h-fasted wild-type and lipl-1lipl-3 mutant animals (11,500×) show that the lipl mutants have more lipid-droplet stores in ad libitum fed and fasted conditions. Quantification of vesicle number and size is depicted as mean+s.e.m., n = 4 independent experiments.
Confocal images of HeLa cells stained with NF45/NF90 antibodies and antibodies against nucleolin and fibrillarin. Scale bar, 10 μm.
A Prox1a and Eng expression in the myotome of 30hpf wild type and MZgrk2 embryos injected with mRNAs encoding Shh, dnPKA or mSmoA1-GFP. Each panel shows Prox1a in green, Eng in red, and the merged images with DAPI staining in blue. The co-labelling for Prox1a and Eng (orange) is indicative of MP differentiation (n=30 for each sample) Scale bar, 50μm.
(i,j) Mcip1.4 (i) and atrogin-1 (j) mRNA levels in WT and miR-212/132 null (KO) mice 3 weeks after transaortic constriction (TAC) or Sham operation (n=5-7 per group). All values represent mean±s.e.m. *P0.05; **P0.01; ***P0.005. #P0.05 compared with WT TAC. FC, fold change.
(D) Schematic of miRNA-binding site (MBS) enrichment. PTX mediated synaptic downscaling might lead to a local increase in miRNA abundance or activity. These effects can be potentially captured by testing for an enrichment of MBS in 3'UTRs of downregulated genes in comparison to the sequencing background (expressed genes).
C. (a) Pictures of the tumors in all groups in B. (b) Further validation of the effect of pep-AP in vivo.
C, D) OCT-A imaging of LIF-treated mouse retina. Adult mice were intravitreally injected with 1 μl of LIF (50 ng, Sigma) or vehicle solution (PBS). Retinal OCT-A images were obtained 7 days after the injection and representative images are shown. Blood vessel density was determined as percentage of vessel-covered area/total area surface using ImageJ software and shown in D), n=7-8. Data information: Bars and error bars represent mean ± SEM. All experiments were carried out in three independent studies. Two-way ANOVA was used as statistical test.
A+B. Images showing representative HEK S1/S2-/- cells co expressing YFP-STIM1 (green) or either STIM1-mCherry or STIM1A-mCherry (red) and merged images before (A) and after (B) stimulation with TG.
A The effect of PH compounds was analysed using clonal lines bearing single copy integrations of the mini-dual fluorescent HIV-1 LTR reporter, md-HIV, where GFP is constitutively expressed from the EIF-1α internal promoter, and DsRed from the 5' LTR.
PCA was conducted on global gene activity in mouse fetal tissue at day 0 and 42, mouse E19 organoids at day 3 and 30 of culture, mouse adult organoids at day 3 and 30 of culture (n=4 independent intestinal tissue specimens and n=4 independent organoid cultures).
A The sequences of the isolated VHH antibodies (49 anti-RBD and 10 anti-S1ΔRBD nanobodies) were aligned using Clustal Omega (Sievers et al., 2011). The circular phylogram was reconstructed with Dendroscope (Huson and Scornavacca, 2012). Where applicable, sequence classes are indicated. The anti-RBD nanobodies are colored according to the two RBD epitopes identified in Fig 5 (with epitope 1 in green, epitope 2 in red, and asterisks marking nanobodies included in Fig 5). Anti-S1ΔRBD nanobodies are colored in magenta. VHH antibodies that did not neutralize SARS-CoV-2 are shown in parentheses.
A Protein synthesis determined via leucine incorporation, n = 2-4 independent experiments. *P = 0.03 versus Ad-cont, §P = 0.06 versus Ad-cont.
Biological process pathways identified by DAVID as enriched for Class 1 or Class 2 genes hyperacetylated in low- or high-migrating cells, respectively (adj. P-value < 0.05 for Class 1 and P-value < 0.05 for Class 2). Dots represent GO term enrichment with color coding: red for high enrichment, blue for low enrichment, and sizes of the dots representing the significance score of each subset (the bigger the dot, the higher its significance).
I. Survival (percentage) of female Canton-S Drosophila with and without supplementation of ALA as indicated. The numbers of quantified flies: 100 (Canton-S + 0 mM ALA), 100 (Canton-S + 0.5 mM ALA). Three independent experiments were conducted. J. Survival (percentage) of female Canton-S Drosophila with and without supplementation of ALA at 26-day as indicated. The numbers of quantified flies: 100 (Canton-S + 0 mM ALA) and 100 (Canton-S + 0.5 mM ALA). Three independent experiments were conducted. Data information: Error bars represent SDs. p-values for lifespan curves ( were calculated by the log-rank test. The statistical tests used in other panels were student's t-tests. *p < 0.05, **p < 0.01, ***p < 0.001, ****p < 0.0001, and non-significant (NS) represents p > 0.05.
(i) Graphical summary: Through a combination of experimental and computational work we characterised the HES5 dynamic expression in the mouse E10.5 ventral spinal cord. We found evidence that progenitors located in two domains (motorneuron, MN and interneuron, IN) give rise to distinct spatiotemporal characteristics that are indicative of differences in coupling strength and can explain increased differentiation rates observed in MN.
C,D. Co-immunofluorescence staining of ER (CLIMP-63, green) and lysosomes (TMEM192-HA, red) in control and Sh-FAM134B U2OS cells over-expressing TFEB S142A:S211A-GFP (purple). BaFA1 was used at 100 nM for 4h. Scale bar 15 μm and 2 μm (higher magnification boxes) (C). In (D), Quantification of CLIMP63 fluorescence in TMEM192-HA decorated lysosomes. Mean +/- standard error of the mean (sem) of N=3 biological replicates. N= 21 (vehicle ctrl), N=33 (TFEB S142A:S211A-GFP ctrl), N=21 (vehicle shFAM134B), N= 30 (TFEB S142A:S211A-GFP shFAM134B) cells were analysed. Student's un-paired T-test ***p<0.0005; NS not significant.
(B) Elastic-Van Gieson (EVG) staining of human coronary arteries demonstrating various degrees of atherosclerosis.
(G) Transmission electron micrographs of A. castellanii infected with L. pneumophila. A. castellanii was infected (MOI 5, 42 h) with L. pneumophila wild-type strain JR32 and subjected to high-pressure freezing and electron microscopy. Many LCVs were still intact at 42 h post infection (left panel; arrow: intact LCV membrane, arrowhead plasma membrane), and occasionally, the bacteria were flagellated (middle panel, arrow). Some LCVs were already ruptured, and the bacteria were released into the host cell cytosol (right panel; arrows: ruptured LCV membrane). Scale bars: 2 µm, 0.5 µm (insets).
Same as in (A) but cells were fed with 8 µg of A9M peptide bead and exposed to 12.64-Luc Reporter T cells. Experiments were combined by normalizing RLU values to the average of the negative control I-Ab. Error bars show SD of 3 independent experiments. * p < 0.05 for Rab39a or β2m siRNA vs negative control I-Ab using ANOVA
Quantitative mass spectrometry analysis of affinity purified Dpb11 complexes, comparing Dpb11 purified from rad9∆ cells with or without the 9-1-1 subunit Ddc1. Cells were grown in the presence of 0.04% MMS. Error bars represent SEM of selected proteins for which there were 2 or more peptide-spectrum matches (PSMs).
F. Immunofluorescence of FLAG (green) and pERK1/2 (grey) in oocytes after injection of different MOS variant mRNAs combined with mCherry mRNAs. The signal of mCherry was directly captured after fixation, with DAPI staining for DNA visualization (blue). (n=over 30 oocytes in each group). Scale bar=10 µm.
A HEK293 cells were transiently transfected with the indicated GFP fusion constructs encoding full‐length or indicated fragments of USP45. Thirty‐six hours post‐transfection cells were lysed and GFP immunoprecipitated. The immunoprecipitates were resolved on a polyacrylamide gel and stained with Instant Blue or subjected to immunoblotting with the indicated antibodies. GFP empty vector was used as a negative control.
A. HeLa cells, untreated or treated with SA, were fixed and visualized by fluorescence microscopy using anti-Sec24C Ab, anti-eIF3 Ab, and DAPI (blue). Data information: Scale bars, 10 µm.
Mice were intranasally given 1011 vg of AAV-vector in 50 µl volume three times in three-week intervals. 20 µg of Cal/7/9 WIV per 50 µl was given i.n. two times. Blood samples were taken at indicated time points (red drops). After influenza challenge, mice were monitored for survival and weight loss for two weeks before necropsy.
E) Sholl analysis of primary cortical neurons of WT and Mfn2 KO mice co-transfected at DIV4 with GFP and the indicated plasmids.
A. Telomere length for clone 35 upon POT1 removal and depletion of selected recombination proteins with siRNA (pulsed-field gel electrophoresis).