EMBO/sd-character-level-ner huggingface dataset:
A-C Line charts showing in vivo growth of HBECs as measured by radiance after implantation of either control or different progestogen-containing pellets. Points show means of radiance in individual glands ± SEM. Statistical significance was tested by fitting a mixed effect linear model with random effects to the log10-transformed data; n=87 and 64 respectively for control and progesterone, n=34 respectively for both control and DSG, n=59 and 39 respectively for control and GSN, n=70 and 79 respectively for control and LNG, n=33 and 20 respectively for control and CMA, n=28 and 30 respectively for both control and CPA, n=48 and 35 respectively for control and DSP and shown by asterisks next to legend . To test differences at endpoint Wilcoxon rank-sum test was applied on log-transformed fold change values, asterisks at endpoints of graphs.
D. FSC of the electron density map of the T4SS3-10+D4 complex. The 0.5 line crosses the FSC at a resolution of 28 Å.
C, D & E. Residual level information of key amino acids interacting with actin monomers from ABD1: I22, H29 (C); ABD2: N109 (D)
(C, D) Immunoblot analysis of AGIA-GgPLZF (C) or -GgSALL4 (D) in FLAG-GgCRBN-WT or -GgCRBN-I390V expressing CRBN-/- HEK293T cells treated with DMSO or thalidomide (Tha) for 16 h. (E, F) Immunoblot analysis of AGIA-Mm PLZF (E) or -MmSALL4 (F) in FLAG-MmCRBN-WT expressing CRBN-/- HEK293T cells treated with indicated concentration of DMSO, thalidomide (Tha) or 5-hydroxythalidomide (5-HT) for 16 h. (G, H) Immunoblot analysis of AGIA-GgPLZF (G) or -GgSALL4 (H) in FLAG-GgCRBN-WT expressing CRBN-/- HEK293T cells treated with indicated concentration of DMSO, thalidomide (Tha) or 5-hydroxythalidomide (5-HT) for 16 h. Data information: Data in bar graphs were calculated as relative (Gg or Mm) PLZF or SALL4 band intensity with (Gg or Mm) PLZF or SALL4, respectively. The band intensity of DMSO was 100. Error bars denote ± standard deviation (n = 3). P-values were calculated by one-way ANOVA with Tukey's post-hoc test (NS = Not Significant, *P < 0.05, **P < 0.01, ***P < 0.001, and ****P < 0.0001).
(E) Measurement of ATP levels in peripheral muscles of mdx mice after single intravenous injection of MOTS-c (500 μg) (n=6; *p<0.05).
Western blot analysis of Crebh protein in 9-week-old mice (n=3 per group, 2 independent repeats). WT mice injected i.p. with tunicamycin (Tm, 1.5 µg/g body weight) for 72 hours were included as a control. Hsp90 loading controls for Western blot analysis.
(c) HeLa cells, transfected with siGLO or siRNAs for calpain 1 or calpain 2 for 96 h, were analyzed with anti-calpain 1 or anti-calpain 2 domain III antibodies.
A. Four-way plot (t-statistics) presenting the ERK7-dependent fasting-responsive genes (adj.p.val < 0.05). Dark blue indicates significant in both comparisons; dark turquoise, significant in one comparison; light turquoise, not significant.
(C) Amino acids 263-281 retain the full potential of TMEM59 ID to promote HA-LC3 conversion. 293 cells were transfected with the shown CD16:7 chimeras, HA-LC3A or HA-LC3B (as indicated) and GST, and subjected to anti‐CD16 aggregation before lysing them for western blotting. The lower panels show control WBs (unaggregated samples).
b, Peptide hydrolysis activity of 20S and 26Sproteasomes. Homogenates from P28Atg7flox/+; nestin-Cre (blue) and Atg7flox/flox; nestin-Cre (pink) brains were fractionated by glyceroldensity gradient centrifugation (10-40% glycerol from fraction 1 to fraction 30). Aliquots from each fraction were used for the assay of chymotryptic activity of proteasomes using Suc-LLVY-AMC as a substrate in the absence (top) or presence (bottom) of 0.05% SDS. The sedimenting positions of 20S and 26Sproteasomes are indicated with arrowheads. Note that whereas 26Sproteasomes exist in active forms in tissues, 20Sproteasomes are latent and are activated artificially by a low concentration of SDS.
A. Heatmap showing motif activity inferred from differential chromatin accessibility of stage 10½ - AC -DMZ.
E. EB K8-eYFP embryo stained for eYFP (yellow) and E-cadherin (white) (n=7) (Top). Dashed white area zoom on an amnion region which highlights the two cell layers (Bottom).
(B) ROC curves indicate the recovery of 7 true-positive drug-target interactions within the dataset compared to the number of false discoveries from the remaining 1280 drugs within the dataset. The recovery of expected interactions is shown using Spearman correlation, Pearon correlation, and cosine similarity. These similarity metrics allow for an area under the curve of 0.72, 0.84, and 0.66 for those similarity metrics respectively
(B) Scatter plot and heat map of differential gene expression between cre control and Abca12tm1d mice at 8 weeks of age. Legend indicates Log2 fold change values.
(A The kinetics of release of SARS-CoV-2 progeny was assessed from samples obtained from a wash of the apical face of the chip and the vascular effluent (A) collected at each day-post infection. (A) The number of viral genomes in each sample was quantified using a one-step qRT-PCR assay for the SARS-CoV-2 N gene. The starting inoculum introduced to the apical side (labelled 'Inn') corresponded to 200-300 PFU. Lines join datapoints from the same LoC, reconstituted with (green squares) and without (dark blue circles) macrophages. Viral genome numbers within the apical wash showed a declining trend over 3 days of infection. Viral genomes are not detected ('nd') in the vascular effluent for all the chips shown. Data information: In all plots, the bars represent the mean value, and the error bars represent the standard deviation, the solid black line in (A) represents the median.
d, Pearson correlation plot for overlapping candidates from PANC-1 experiments (86 proteins, comparing experiment 2 with experiment 3). x axis: log2(H:L) PANC-1 experiment 3 (L-wortmannin:H-chloroquine 16 h) value; y axis: log2(H:L) PANC-1 experiment 2 (L-wortmannin: H-chloroquine 16 h) value.
Forward migration index (FMI) along the y- and x-axes during cell migration. n = 90 cells per group. Data represent mean ± SEM. **p < 0.01; ***p < 0.001; NS, not significant, by Tukey-Kramer test.
Three-dimensional reconstruction of RNC FtsQ:SecYEG-ND complex. Primary structural elements of the ribosome and SecYEG-ND are indicated. Local resolution map of SecYEG-ND sub-particle. The cytoplasmic side of the translocon demonstrates higher resolution due to stabilization by the bound ribosome, while high-resolution at the periplasmic side is hindered by the SecYEG-ND dynamics within the complex. The associated ribosome is not shown for clarity. A planar slice through the SecYEG-ND core at different signal levels (blue/green/red) with indicated positions of SecYEG TMHs (SecY indicated in orange, SecE in purple, and SecG in green). A single helical turn could be fitted in a density in the area where SecG TMH 1 was expected (green asterisk).
D Representative H&amp;amp;E‐stained sections as well as immunohistochemistry detection of HA‐NFATc1 and p53 in well‐ and poorly differentiated pancreatic tissues of KNCmice. Scale bars, 100 μm.E Quantification of p53 expression with respect to the tumor grading by evaluating both the intensity of immunostaining and the number of cells with overexpression by means of an immunoreactivity score (IRS) in KNCmice (every dot represents one mouse).
D. Immunohistochemistry analysis of Oct4 expression in wild-type, Homo-11, Ts6, Ts8, Ts11, or Ts15 ES cellteratomas produced via the injection of 5×105 ES cells. Scale bar, 100 μm.
Images of mESCs transduced with Eif4a1, Eif4e and Eif4g1 shRNAs in SL. Scale bar, 400 µm.
PD-L1 expression on MC38 and KPC cells 48 hours following 10Gy irradiation in tissue culture (A,B) or 10 Gy irradiation of tumours (C,D) analysed by flow cytometry. Data presented as mean SEM and analysed by Mann-Witney (n=3, A,B). Data presented as mean SEM and analysed by unpaired t-test (n=5 mice/group, C,D).
E RT-qPCR of Abca1 expression from LXR+/+ versus LXR−/− BMMs. Ligand stimulations were performed for 4 h with vehicle control, 1 μM T0901317, or 1 μM T0901317 together with 6 μg/ml PolyIC. Fold changes are shown relative to vehicle‐stimulated LXR+/+. Error bars represent ± SEM for n = 4 (**P = 0.004, *P = 0.012 versus T0901317).
(A) Immunofluorescence analysis of DSBs associated foci as marked by γH2AX in lung adenocarcinoma (A549) cells, cultured either in low glucose (5.5mM, left panel) or high glucose (30mM, right panel) for 5 days, then treated with etoposide (5µM for 60 minutes). The resolution of DNA-DSBs foci, as marked by γH2AX was monitored over 24 hours after drug treatment, CML (marked in green) served as induction control (scale 10µm). (B) Mean percentage of DSBs positive nuclei as evidenced by γH2AX positivity after pre-treatment of different reducing carbohydrates at 0, 3 or 24 hours. More than 400 cells were analyzed for each bar (mean ± SD, : p<0.01;: p<0.001).
(B) The graph shows the mean ± s.e.m. of the percentage of nuclear TFEB translocation in Ezrin-inhibited cells compared to control; n=3 independent experiments were performed. Mann and Whitney test (NSC668394 and stv vs DMSO; siEZR vs siCTRL) *p ≤ 0.05.
(B) Summary of doses, steady-state effects on Aβ40 in brain (% compared to vehicle-treated mice) and the ratios between total skin concentrations of CNP520 and NB-360 and their respective IC50 values for inhibition of BACE-2 in vitro.
(B) The percentage of F4/80+ macrophages cells and rRv2626c-CA-His or its mutants were found in the spleen or lung using Fluorescence-activated cell sorting analysis in the background of CLP-induced sepsis.
(A) Waterfall plot showing the percentage of tumor volume change in olaparib-treated tumors compared to the tumor volume on day 1. +20% and -30% are marked by doted lines to indicate the range of PR, SD and PD. The box underneath summarizes different characteristics of each model and the clinical context at the moment of PDX implantation. TNBC, Triple Negative Breast Cancer; ER+BC, Estrogen Receptor positive Breast Cancer; P, primary; M, metastasis. Error bars indicate SEM from independent tumors (n ≥ 3).
(R) Percentage of LGG-1 puncta colocalized with SQST-1 aggregates in indicated autophagy mutants. Comma-stage embryos were examined for atg-9 and atg-9;epg-7 mutants. ∼200-cell stage embryos were examined for other autophagy mutants.
(C) WT and FAK−/− PEMs were incubated with S. typhimurium strain ΔinvG for a total of 5 hours before analysis with antibodies recognizing LC3. DAPI was used to visualize nuclei and bacteria. Bars represent 10 µm. White boxes show enlarged regions in inset panels, bars represent 2 µm. White arrowheads indicate LC3-negative bacteria, yellow arrow heads indicate LC3-positive bacteria (panels c, f). Yellow arrowhead in panel f denotes an LC3+ cluster of bacteria. (D) The percentage of ΔinvG (first grouping) or ΔΣΠΙ1ΔΣΠΙ2 (second grouping) Salmonella co-localizing with LC3 at the indicated time points is displayed. At least 100 bacteria were counted per condition per time point. Values are means ± SEM, N = 3, *p<0.05.
The expression of Il1b was measured in whole brain using quantitative PCR 1 hour, 2 hours and 6 hours after I.P. challenge (n=6 mice per group). Data are expressed as mean ± STDEV and were tested by two-way ANOVA with Bonferroni's post-test; *P<0.05, **P<0.01, ***P<0.001. Symbols above bars are versus PBS at the relevant time-point.
ELISA quantification of IgM (H) and IgG (I) in serum from immunized adoptively transferred mice. The graph shows the mean serum concentration of IgM and IgG from n ≥ 5 reconstituted mice, respectively ± SEM.
H&E staining of back skin sections from mice treated intradermally with Control or Clodronate liposomes. n= 3 - 4 skin samples per mouse, n= 3 - 4 mice. Scale bar, 200 μm. epi, epidermis; der, dermis.
(E) WT, Pml-/-, Mk2-/- and Pml-/-Mk2 -/- BMDMs were treated with zVAD (20 μM) and AT-406 (1 μM) for the indicated timeframes. The levels of RIPK1, p-RIPK1[S166], RIPK3, p-RIPK3, MLKL, and p-MLKL in cell lysates were analysed by immunoblots. Results are representative of three biological replicates.
Attachment of Tau condensates to negatively-charged (glutamate treated) glass surfaces. Tau:RNA and Tau:PEG:RNA condensates show pronounced surface wetting, whereas Tau:PEG condensates stay in solution or show partial wetting. p-Tau:PEG condensates also wet the surfaces. Scale bars=10 μm.
p53 inhibition induces autophagy by ER stress (a-c) WT HCT116 cells were transiently transfected with GFP-LC3, treated with PFT-α for 2, 4 or 6 h and subjected to immunofluorescence staining to observe the colocalization of GFP-LC3+ puncta with the ER marker ERp57 (a) or a mitochondrial marker Complex III (b). Note that cells with GFP-LC3+ puncta often contain scarce amounts of ERp57 (white arrows) after prolonged incubation with PFT-α. The percentage of colocalization (means ± s.d., n = 3 experiments with 50 images per experiment) was determined by confocal microscopy (c).
(C) Control and GRASP55 KO cells were transfected for 16 hours with GCS-HA or LCS-HA and processed for cryoimmunolabeling with anti-HA antibody (10-nm gold particles) and anti-GM130 antibody (15-nm gold particles) in case of GCS-HA and anti-HA antibody (15-nm gold particles) and anti-GM130 antibody (10-nm gold particles) in case of LCS-HA. Representative images of the distribution of GCS-HA and LCS-HA are shown. Scale bar 200nm. Red asterisk marks C4 cisterna and blue circles indicate GM130 labelling.
(A) Phylogenetic relationship of UbL domains in S. cerevisiae and schematic representations of the corresponding UbL proteins. Sequences were clustered and mapped onto a N-J tree by ClustalX2 and the PHYLIP package. ASP, aspartyl protease domain; UBA, ubiquitin-associated domain; USP, ubiquitin-specific protease domain; DD, dimerization domain; RBD, Rad4-binding domain; ST2, Sti1/Sti1 pair;
HCT116 cells were transiently transfected with the expression plasmids as indicated. After 36 hr post-transfection, cells were treated with H2O2 (500μM) stimulation (I) for 1hr and then collected for immunoprecipitation and western blotting analysis. Immunoprecipitation was performed using anti-Beclin 1 antibody followed by immunoblotting with anti-Flag or anti-Beclin 1 antibody.
E Macrophage-specific knockdown of CG9005 by UAS-RNAi lines. n=22, 20, 21, 23, 35, 28 embryos. p<0.0001 for all comparisons. Data information: Throughout paper mac> indicates GAL4 driven expression of a UAS construct specifically in macrophages by srpHemo-GAL4. N for movies represents imaging from different embryos. Unpaired t-tests. Graphs show mean±SEM; ns=p>0.05, *p<0.05, ****p<0.0001.
Bioinformatic prediction of IGF2R and CD20 cross-reactivity. The structure of IGF2R (in red) and IGF2 (green) are shown compared to docking poses of epitope 3. These data show that the helical region (residues 178-184) of the epitope mediates binding to the receptor as well as IGF2. The C-terminal helix of epitope 3 partially overlaps the first α-helix of IGF2. Cluspro-dock IGF2R-CD20 binding epitope poses corresponding to PDB codes 2v5p-2oslP, 2v5p-2oslQ and 2v5p-3pp4P are coloured in yellow, blue and cyan, respectively (c).
(D) Detailed structures of GM3 species: sialyllactose head group, sphingoid base (d18:1), typical fatty-acid lengths (LCFA, VLCFA), and acyl chain modifications (α-hydroxylation, ω-9 desaturation).
B. Proposed catalytic mechanism for isopeptide bond cleavage catalyzed by MvcA. Nucleophile attack of the isopeptide bond by the thiol from the catalytic center of MvcA leads to the release of UBE2N and formation of a thioester linked MvcA-Ub intermediate, which is further attacked by a nucleophilic water to produce UbQ40E and to regenerate the active enzyme.
A-C. Iba1 was used as a marker for microglia and PIP2 levels were detected by measuring the intensity of florescence per cell. The average fluorescence was calculated above background in the cortex and hippocampus at 2 (A), 6 (B) and 9 (C) months. All data shows the mean±SD of 3 independent experiments analysed using 2 way ANOVA with Sidak's multiple comparison tests performed **=p<0.01, ****=p<0.0001.
Five orthotopic xenograft mice models were established from four different MPNSTs and one cell line. Two of the MPNSTs come from the same NF1 patient; the other two were sporadic cases. Primary tumor (2-3 mm3) or tumor cell line (3 × 106 cells) were grafted or injected in the leg of athymic nude mice, close to the sciatic nerve. Tumors were perpetuated along several passages and subsequently expanded. Several assays were performed on tumors in early passages (histopathological analysis, gene expression profiling, genomic profiling, and drug efficacy studies). *NF1-MPNST-001 at passage 4 (P4) and all primary tumors and orthotopic tumors (OT) at passage 1 (P1) were analyzed by exome sequencing and immunohistochemistry. All primary tumors and orthotopic tumors at passages 1 and 4 were analyzed by expression array (except NF1-MPNST-001 PT, SP-MPNST-001 OT P4, and NF1-S462 OT P4). Copy number analysis (CNA) was performed in all samples.
E. Proportion of stalled forks (CldU-only tracks) among DNA fibers from (C) (bars, mean; 200 fibers analyzed per condition; n=2 independent experiments).
B The effect of increasing levels of PS on the ATPase activity of ATP8A2 (WT and I376M)‐CDC50A complex.
B. Mass cytometry was performed on PBMCs obtained from acute asymptomatic (n=19) and acute symptomatic (n=37) COVID-19 patients and healthy donors (n=10). Monocytes were characterized based on their CD14 and CD16 expression. Data are presented as Mean ± SD **P<0.01; ***P<0.001 (Kruskal-Wallis test with Dunn's multiple comparison). C. Classical, intermediate and non-classical monocytes were further defined in acute asymptomatic (n=19) and acute symptomatic (n=37) COVID-19 patients and healthy donors (n=10) with inflammatory marker CD169. Data are presented as Mean ± SD **P<0.01; ***P<0.001 (Kruskal-Wallis test with Dunn's multiple comparison).
Representative images of wild-type and mutant cells organized by marker and phenotype (labels on the left of each panel). For each phenotype, three cells labelled for the training set (labelled single cells) and cells identified by the 2NN classifier (identified single cells) are shown. The table to the right of the images shows (from left to right): [1] the occurrence of each phenotype in a wild-type population (% in WT); [2] the number of specific phenotype mutants (all) and stringent specific phenotype mutants (str) for each of the 17 mutant morphologies; [3] the most significantly enriched GO Slim biological process and; [4] the most significantly enriched protein complex. # denotes term below statistical significance.
, LN229, T98G, U87, U87-EGFRvIII and HCT116 cells were treated with increasing concentrations of LXR623 for 72h. Thereafter, protein lysates were collected and subjected to standard western blot (LN229, T98G and U87) or capillary electrophoresis (U87-EGFR-vIII and HCT116) for the expression of Usp9X, Mcl-1, Bcl-2, Bcl-xL, Noxa, BIM and/or Actin and Vinculin. In U87-EGFRvIII and HCT116, Vinculin was used in lieu of Actin.
(C) Experimental probability density function (PDF) of unbinding forces (in pN) determined by SMFS (black line, measured data). The three distinct maxima fitted by a multi-Gaussian function reveal rupture of a single bond (blue dotted line), or simultaneous rupture of 2 (red dotted line) and 3 (green dotted line) bonds, respectively.
ST2 wild type or NEMO KO cells were stimulated for 15 minutes with SF-IL-17 (500 ng/ml), solubilized and IL-17RSC was isolated via consecutive Flag and Strep immunoprecipitation and analyzed by MS. (B) The ratio between iBAQ intensities of selected IL-17RSC components to iBAQ intensity of IL-17RC. Mean + SEM from two independent experiments is shown.
F Mitophagy assay was monitored by the degradation of Om45‐GFP and analyzed for GFP cleavage by immunoblotting.
C. Immunocytochemistry of VAMP8 imaged at the plasma membrane using TIRF microscopy, following 4 minutes of antigen stimulation. Endogenous VAMP8 was knocked down with siRNA. Expressed wild type VAMP8 and VAMP8Ala (T47A, T53A, S54A) quickly assumed a uniform plasma membrane stain (due to VAMP8 vesicles fusion), whereas VAMP8Glu (T47E, T53E, S54E) showed a punctate stain, representing vesicles docked at the plasma membrane without fusion. Scale bar 10 µm.D. Identification of puncta in TIRF immunocytochemistry images using MATLAB (see Method). Identified puncta are shown in white in the middle image. Scale bar 10 µm.
(A) Identification of GmLMM1-interacting proteins by IP-MS analysis. GmLMM1-FLAG was transiently expressed in Arabidopsis protoplasts, purified by anti-FLAG M2 agarose, and subjected to mass spectrometry analysis. The complete list is shown in the source data.
E, F (E) Epifluorescence microscopy imaging and (F) quantification of ASC speck formation in BMDMs from ASC-mCitrine (Green) transgenic mice. Cells were primed with LPS (200 ng ml−1, 150 min), pre-treated with VX-765 (50 µM, 30 min), then treated with VHHASC, VHHmASC (100 µg ml−1) or CRID3 (50 µM) for another 30 min before stimulation with nigericin (top), or PFO (bottom) for 2h and finally fixed with 4% PFA and nuclei stained with DRAQ5 (Blue). Scale bars: 100 μm. Images in (E) are representative of one out of three independent experiments that were quantified in F. Data is displayed as floating bars with the max/min values and mean (thicker band).
(E) Ectopic expression of Gadd45b-Myc-Flag slightly inhibited LY294002-induced HSV-1 DNA synthesis. Latent cultures were transduced with Gadd45b for 3 days and then treated with LY294002 and WAY-150138. Total DNA were collected at the indicated times (LY treatment for 18 or 72 hours) post-reactivation in the presence or absence of Gadd45b-Myc-Flag. The relative levels of viral genomic DNA were determined by qPCR using primers for the HSV-1 UL44 gene. Input DNA was normalized by qPCR detection of the rat RPL19 gene. 3 biological replicates. The bars and error bars are mean ± SD. Data information: P values equal to or less than 0.05 were considered significant, asterisks denote statistical significance (*, p<0.05; ***, p<0.001; ****, p<0.0001). P values are calculated using two-tailed unpaired Student's t test. P values > 0.05 were not significant (ns).
C Phospho-ERK1/2 levels in control and KA-treated WT (both n=6) and Fxr2 KO mice (both n=6) sacrificed at different time intervals [0, 20, 40 and 60 min]. * adjusted p < 0.05, ** adjusted p < 0.01 (two-way ANOVA: main effect for genotype: F1,40 = 5.99, p < 0.05; interaction effect genotype and time; F3,40 = 4.11, p = 0.012; p < 0.05 and p < 0.01 with Bonferroni correction for 40 and 60 min, respectively). Data are presented as mean ± SEM.
(B) CHD1 is recruited to an I-SceI-induced DSB site and is co-localized with γH2AX. Immunofluorescence studies using U2OS19 ptight13 GFP-LacR cells containing a stably integrated I-SceI cleavage site flanked by 256 copies of lac operator (lacO) on one side and 96 copies of the tetracycline response element on the other side (tetO). The localization of the GFP-lac repressor protein (GFP-LacR) at the lac-operator DNA sequences in the nucleus before (− I-SceI) and 16 h after I-SceI-induced (+ I-SceI) DSB. After 16 h of doxy treatment, CHD1 and γH2AX co-localized at I-SceI cleavage site, along with DNA-bound GFP-LacR but not in uninduced cells (−I-SceI). Scale bar 10 µm.
J RT-qPCR analysis of viral RNA levels in mouse primary splenocytes infected with VSV/H1N1/SeV (MOI=1.0, 24 hrs) immediately after addition of NaCl (+17, 34 and 51 mM). Data information: Data show the mean and SD of three biological replicates. For all statistical testing, p values were calculated using two-tailed unpaired Student's t-test. NS, not significant (p > 0.05). *p < 0.05, **p < 0.01 and ***p < 0.001.
D Heatmap of signature gene expression, from scRNA seq data. Average activities of gene signatures are given as log fold-change for preferred treatment condition, after normalization to DMSO control condition. Range of color scale was adjusted for each signature.
C Confocal images of HeLa cells transiently expressing GFP-CbpCT4 and mCherry-LC3 (upper). The fluorescence intensities of GFP-CbpCT4 (green) and mCherry-LC3 (red) along the arrow are shown in the graph at the bottom.