EMBO/sd-character-level-ner huggingface dataset:
Heat shock-induced changes in protein thermal stability.Figure 5A: Experimental design to measure changes in thermal stability. Samples treated with either heat shock or mock shock are aliquot for treatment with temperatures that denature and aggregate all proteins. Samples are lysed with mild detergent (NP-40) and after tryptic digestion peptides from soluble protein fraction are labelled with TMT labels. The labelling is conducted so that samples from two adjacent temperature treatments are pooled and each TMT set is analyzed by mass spectrometer. At each temperature, the amount of protein still soluble is quantified and the fold change (FC) between heat shock and mock shock is calculated (see 'Materials and Methods' for details). Fold changes in each temperature are summed after adjustment for heat shock-induced aggregation. Fold change-based thermal stability measures are finally transformed to scores for thermal stability B: Volcano plot for the score for thermal stability. Significant (see 'Materials and Methods') heat shock-induced stabilization and destabilization are indicated with blue and red, respectively. Proteins that aggregate in heat shock (as defined in Figure 2A) are shown in black - aggregators with the strongest stabilization are annotated. Members of stress-activated MAPK pathway highlighted in green - alternative names for MAP-kinases are shown in parenthesis. Boxplot on top compares stability scores of aggregators (as defined in Figure 2A and other proteins). The p-value is for non-parametric Wilcoxon test. C Schematic for the structure of stress-activated MAPK pathway (adapted from (Hotamisligil & Davis, 2016) and (Davis, 2000)) with the two branches of MAP-kinases (p38 and JNK) and their upstream kinases (MKK3, MKK4, MKK6 and MKK7). Arrows show the target MAPK branch for each MAPKK. The role of MAP2K4 in p38 phosphorylation is unclear (Hotamisligil & Davis, 2016) and is presented with dashed line. Changes in thermal stability after heat shock are marked with ovals. D Thermal stability changes in protein complex members. Scores for thermal stability shown for proteins from 26S proteasome (separately for 19S regulatory and 20S core particles) and CCT chaperonin complex. Boxplots indicate median, first and third quartiles with whiskers extended to 1.5 times the interquartile range out from each quartile. Data used in stability score calculation is from two (mock shock) and three (heat shock) biological replicates.
Figure 6raphical representation of the expected transcriptome changes with regard to Alu RNA expression and processing levels based on previous findings in mouse (Appendix Figure S1) and prior reports on the ability of Alu RNAs to control transcription (Mariner et al., 2008; Ponicsan et al., 2010; Yakovchuk et al., 2009) and become self-cleaved (Hernandez et al., 2020). Association between SINE Alu RNA ratio (upper panel) and gene expression levels (lower panel) of genes up-regulated in AD (Dataset EV3, |log2FoldChange|> 0.5). Every column in both panels corresponds to the same MAP patient of either the no AD or AD group. Patients in each group are sorted from left to right in an ascending order with regard to Alu RNA processing ratio. Every row in the heatmap corresponds to one gene, with color density representing normalized FPKM values from RNA-seq for this gene for each patient (columns) (red represents high and blue low expression levels). Association between full length Alu RNA levels (upper panel) and gene expression levels (lower panel) of genes down-regulated in AD (Dataset EV4, |log2FoldChange|> 0.5). Every column in both panels corresponds to the same MAP patient of either the no AD or AD group. Patients in each group are sorted from left to right in an ascending order with regard to full length Alu RNA levels. Every row in the heatmap corresponds to one gene, with color density representing normalized FPKM values from RNA-seq for this gene for each patient (columns) (red represents high and blue low expression levels). Scatterplot depicting the positive correlation between average gene expression values of upregulated genes in Figure 6B and Alu RNA processing ratio in AD patients (r = 0.88, p<0.001). Statistical test is based on Pearson's product moment correlation coefficient and follows a t distribution using the cor.test function in R package stats. Scatterplot depicting the negative correlation between average gene expression values of down-regulated genes in Figure 6C and full length Alu RNA levels in AD patients (r = -0.42, p<0.001). Statistical test as in subfigure 6D.
Hdac1-deficient thymic lymphoma lines require DOT1L activity for survival.Figure 5Representative apoptosis FACS plots of cell lines treated with DMSO or the DOT1L inhibitor SGC-0946 for two days. Annexin V staining and DAPI staining were performed on unpermeabilized cells to distinguish live (Annexin V low; DAPI low), apoptotic (Annexin V high; DAPI low) and dead (Annexin V high; DAPI high) cells. Quantification of several independent FACS experiments, including the experiment shown in panel (A). Mean with individual data points of 2-4 replicates each of two independent lines per genotype. p<0.001 (***) by two-way ANOVA, comparison to corresponding DMSO control.
Figure 4A The overall fold of SiaB/SiaC complex. The two SiaB molecules are shown as cartoons in light blue and pink, respectively. The two SiaC molecules are all shown as cartoons in yellow. ADP and TPO68 are shown as spheres in atomic colors (C, cyan; N, blue; O, red; P, orange). B Detailed interactions between SiaB and SiaC. The interacting residues are showing as sticks. The C-atoms of SiaB and SiaC residues are colored in light blue and yellow, respectively. H-bonds are indicated by black dashed lines. C SiaCE33A partially restored the biofilm formation of ΔsiaA. The biofilm formation by the indicated strains was displayed with crystal violet staining (up) and quantified with optical density measurement (down). D Triple mutation of E61A-Q64A-R67A is important for the function of SiaB. The biofilm formation by the indicated strains was displayed with crystal violet staining (up) and quantified with optical density measurement (down).
Fig.Figure 7A Birthdating of adult-born neurons prior to recombination was conducted in 24-week old mice. For marker expression analysis, BrdU was injected i.p. every 24 hours for three days (B and C); for morphology analysis, CAG-RFP was stereotactically injected into the DG (D-G). Tamoxifen was applied i.p. every 12 hours for five days. Mice were sacrificed 3dpT and 13dpT. B Representative images of recombined (GFP+, green) BrdU+ (grey) neurons in 24-week old control and β-catex3 iDCX animals at 13dpT expressing the stage specific markers DCX (red) for immature neurons and Calbindin (red) for mature neurons. Arrows and arrowheads indicate marker negative and marker positive cells, respectively. Scale bar= 10µm. C Quantification of DCX and Calbindin expression in BrdU+ recombined cells. At 13dpT, labeled neurons in β-catex3 iDCX animals show a shift towards a more mature marker profile [DCX p=0.0238, Calbindin p=0.0714] (3dpT: control: n= 4 animals, β-catex3 iDCX: n= 8 animals; 13dpT control: n= 5 animals, β-catex3 iDCX: n= 5 animals). D Representative reconstructions of RFP-birthdated control and β-catex3 iDCX neurons in 24-week old mice at 3dpT. Scale bar= 20µm. E Quantification of dendritic length [p=0.0007], branch points [p=0.3909], and Sholl analysis [p=0.0001] showed increased complexity of birthdated β-catex3 iDCX cells at 3dpT (control: n= 20 cells from 4 animals, β-catex3 iDCX: n= 19 cells from 5 animals). F Representative reconstructions of RFP-birthdated control and β-catex3 iDCX neurons in 24-week old mice at 13dpT. Scale bar= 20µm. G Quantification of dendritic length [p=0.1857], branch points [p=0.1331], and Sholl analysis [p=0.1501] showed no difference between β-catex3 iDCX and control cells at 13dpT (control: n= 18 cells from 4 animals, β-catex3 iDCX: n= 20 cells from 4 animals)
Figure 2Hcp release assay. FLAG-tagged Hcp (HcpFL) release was assessed by separating cells (C) and cell-free culture supernatant (S) fractions from 109 cells of the indicated strains. Proteins were separated by 12.5%-acrylamide SDS-PAGE and TolB and HcpFL were immunodetected using anti-TolB (upper panel) and anti-FLAG (lower panel) antibodies. Molecular weight markers (in kDa) are indicated on the left. The experiment was performed in triplicate and a representative result is shown.
Figure 4(A). RIP analysis of pri-let-7a1 and Flag-TruB1 from HEK-293FT cells. RNA was extracted from IP material and analyzed by qRT-PCR. HEK-293FT cells were infected with lentiviruses encoding tetracycline-inducible expression of TruB1, mt1, mt2, or GFP and treated with doxycycline. Error bars show SD; n=3. Significance was assessed using 2‐tailed Student's t‐test, < 0.05*. (B). EMSA of 32p-ATP-labelled pri-let-7a1 or pri-let-7a1 loop mt mixed with recombinant TruB1, mt1 or mt2 at several doses. RNP: Ribonucleoprotein complexes. (C). Design of Flag-labelled TruB1 knock-in (KI) cells. HiBIT and 3 x Flag sequences were inserted into the N-terminus of the TruB1 gene in HEK-293FT cells. (D) Sequencing clusters obtained from HITS-CLIP experiment. Left are for let-7, and right for tRNAs. (E). Tag densities represented as dots. Density of miRNA clusters in HITS-CLIP were normalized by miRNA expression as determined by TaqMan array. (F). The proportions of different types of mapped transcripts from the HITS-CLIP experiment. (G). Sequence motifs from reads mapped to tRNAs from the HITS-CLIP experiment. (H). TruB-modified site in tRNAs. Location of pseudouridine is colored in red. (I). Sequence of the terminal loop in pri-let-7a1. Lin28B binding site is colored in red.
Figure 7WT which carry shRNAs (Oma1 or scramble) and ectopic Mfn1, were stained with TMRE. The percentage of cells that maintained the membrane potential is shown. Values are average ± SD (n = 3). 100-150 cells were analyzed in each experiment. Drp1-KO MEFs which carry shRNAs (Oma1 or scramble) and ectopic Mfn1, were stained with TMRE. The arrows indicate cells that lost the mitochondrial membrane potential in (C). Scale bar, 10 µm. The percentage of cells that maintained the membrane potential is shown. Values are average ± SD (n = 3). 100-150 cells were analyzed in each experiment. OCRs were analyzed in the same set of MEFs. Quantification of the basal OCRs and respiratory capacity is shown. Values are average ± SD (n = 3). OCRs were analyzed in the same set of MEFs. Quantification of the basal OCRs and respiratory capacity is shown. Values are average ± SD (n = 3). (I) Summary of the data.
Figure 5Representative Western blots illustrating the expression of SMC6 and of monoubiquitylated FANCD2 in protein extracts from HeLa cells transfected with the indicated siRNAs and treated 48 hours after transfection with HU (5mM, 18 hours) or Mitomycin C (200 ng/ml, 18 hours). Vinculin is used as loading control. Top. Representative images of nuclei (DAPI stained, blue) with RAD51 (green) foci in HeLa cells transfected with the indicated siRNAs and treated with HU or MMC, as indicated in panel A. The scale bar represents 10 μm. Bottom. Histograms presenting the percentage of RAD51 foci-positive cells as evaluated in the different conditions of above. Data represent the means+/-S.E.M. and were analyzed by unpaired t-test. siSMC6 vs siLacZ: n=3, NT, MMC or HU p=n.s.; siFANCD2 vs siLacZ: n=4, NT p=n.s., MMC p=0.0003, HU p=0.0479; siSMC6+siFANCD2 vs siLacZ: n=3, NT p=n.s., MMC p=0.0439, HU p=0.0458.
Figure 3Left panel: Growth curve was carried out to test smc5 fancm cell proliferation. Data represents means ± SD of 3 experiments. Right panel: Survival curve of smc5 fancm cells treated with different concentrations of cisplatin. Data represents means ± SD of the 3 experiments. Clonogenic assay to test cisplatin sensitivity of smc5 fancm cells in long term assays. Data represents means ± SD of 2 independent experiments with two independent clones analyzed for smc5 fancm. Left panel: Growth curve was carried out to test smc5 rad17 (C) cell proliferation. Data represents means ± SD of 3 experiments. Right panel: Survival curve of smc5 rad17 (C) cells treated with different concentrations of cisplatin. Data represents means ± SD of the 3 experiments. Left panel: Growth curve was carried out to test smc5 ddx11 (D) cell proliferation. Data represents means ± SD of 3 experiments. Right panel: Survival curve of smc5 ddx11 (D) cells treated with different concentrations of cisplatin. Data represents means ± SD of the 3 experiments.
Figure 6(A) Old APPPS1 tissue was cultured alone (old alone, white bars) or incubated with conditioned media (CM) collected from young WT slices (old alone + young CM, grey bars). Analysis included co-culture of old APPPS1 and young WT brain slices (old co-culture, black bars) as a positive control and old APPPS1 tissue incubated with conditioned media collected from old APPPS1 slices (old alone + old CM, white squared bars) as a negative control. Quantitative analysis at 7, 11 and 14 DIV reveals increased numbers of core-only plaques upon incubation of the old APPPS1 tissue with conditioned media collected from young WT slices, fully recapitulating core-only plaque numbers observed in the co-culture. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, each experiment including at least 2 independent slice culture dishes (n.s.= not significant, **P <0.01, ***P < 0.001). (B) Old APPPS1 tissue was incubated with conditioned media collected from young WT slices previously treated with clodronate (old alone + young CM + Clo, grey bars ) and vehicle control (old alone + young CM + Ctr, white bars). Quantitative analysis at 7, 11 and 14 DIV reveals decreased numbers of core-only plaques upon incubation of the old APPPS1 tissue with conditioned media collected from young WT slices pre-treated with Clo. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, each experiment including at least 2 independent slice culture dishes (n.s.= not significant, ***P < 0.001). (C) Old APPPS1 tissue was incubated with conditioned media collected from cultured WT primary microglial cells (old alone + MG CM, grey bar) or with unconditioned slice culture media as a control (old alone + Ctr, white bar). Quantitative analysis of core-only plaques at 14 DIV reveals enhanced amyloid plaque clearance upon incubation of the old APPPS1 tissue with conditioned media collected from cultured primary microglia. The values are expressed as percentages of core-only plaques from the total number of amyloid plaques and represent mean ± SEM from 3 independent experiments, each experiment including 2 independent slice culture dishes (*P < 0.05).
– Specific bacteria and mitochondria ribosomal RNA segments and fractions induce proinflammatory but not type I IFN cytokine production through an endosomal TLR.Figure 1A Cytokine release by PBMCs challenged with heat inactivated S. aureus (hiSa), and/or RNase A (RA) treated solution, or Sa19 (TLR13 activating ORN) upon TLR2 blockade (T2.5; n.p., not performed; **, p ≤ 0.01; n = 3). B Alignment of Sa19 and mitochondrial 16S rRNA Sa19 "like" segment (mt, mitochondrial; PTL, peptidyl transferase loop; D, domain; _, transition region) sequence with common core motif (blue) and uracils (red U); *, conserved in human (Hs), cattle (Bt), mouse and rat; G/A underlined, mutated core motif; ma, 6N methylation of adenosine 7. C Cytokine release of PBMCs transfected with ORNs including TLR7/8 ligand RNA40 (n = 3). D, E Activity of PBMCs upon bacterial RNA challenge, pretreatment with chloroquine in (D) only (S, Svedberg; r, ribosomal; tot, total; n = 3). F Activity of PBMCs upon mitochondrial (mt) RNA challenge (Hs, human; triangle, increasing doses; LFA, Lipofectamine 2000; n = 3). G Activity of PBMCs challenged with ORNs and total S. aureus (Sa) RNA (Myd88d/d, mutant MyD88 expression not impairing LPS driven IL-8 production; n = 2). H Responsiveness of undifferentiated (undiff) and 3- or 8 days PMA differentiated (ddi) THP1 cells to Sa19 challenge (n = 3). I Activity of parental and Unc93b1-/--3ddiTHP-1 cells challenged with ORNs (n = 3).
Curcumin prevents HFD-induced obesity A, B, C Appearance, body weight trajectories and food intake of the mice.Figure 1Appearance of the mice. , body weight trajectories of the mice. food intake of the mice. Representative pictures of iWAT and eWAT. E iWAT, eWAT and liver weights at termination of study. F, G H&E staining and quantification of size of adipocytes of fixed iWAT and eWAT. H Changes in the morphologies of livers and H&E staining depicted steatosis as circular white gaps caused when the dehydration process leaches the fat out of fixed livers. I, J, K Fasting blood glucose, serum triglyceride and FFA levels of mice after 12 weeks on HFD. L, M, N, O The blood glucose level of mice after intraperitoneal injection of glucose or insulin for glucose (GTT) (L) and insulin tolerance tests (ITT) (N), and AUC, area under the curve (M, O).
Genome characterization of nCoV-2019.Fig. 1pie chart showing metagenomics analysis of next-generation sequencing of bronchoalveolar lavage fluid from patient ICU06. b, Genomic organization of nCoV-2019 WIV04. Similarity plot based on the full-length genome sequence of nCoV-2019 WIV04. Full-length genome sequences of SARS-CoV BJ01, bat SARSr-CoV WIV1, bat coronavirus RaTG13 and ZC45 were used as reference sequences. Phylogenetic tree based on nucleotide sequences of complete ORF1b of coronaviruses. Software used and settings can be found in material and method section.
Figure 1(A) DNA damage induces H2AX ADP-ribosylation. 293T cells were treated with H2O2 (2 mM in PBS, 5 minutes), MMS (1 mM in medium, 30 minutes) or mock (PBS, 30 minutes). ADP-ribosylated proteins were IPed with anti-ADP-ribose (anti-ADPR) antibody. ADP-ribosylated H2AX was examined by Western blotting using anti-H2AX antibody. (B) H2AX is ADP-ribosylated at glutamate 141 (E141). shPARG HCT116 cells were treated with H2O2 (2 mM in PBS, 5 minutes) and ADP-ribosylated residues were tagged by a hydroxamic acid derivative with an addition of 15.0109 Da, an increment that can be readily distinguished by mass spectrometry. Fragmentation of the NH2OH-derivatized peptides yielded typical b- and y-ion series, allowing easy localization of ADP-ribosylation sites. Glutamate 141 (E141) is indicated by an asterisk. (C) The E141A mutation abolishes the ADP-ribosylation of H2AX. Empty vector (EV), wild type (WT) or the E141A mutant (E141A) of H2AX was expressed in U2OS H2AX knockout cells that were treated with H2O2. ADP-ribosylated proteins were IPed with anti-ADPR antibody. ADP-ribosylated H2AX was examined by Western blotting using anti-H2AX antibody. (D) ADP-ribosylation on H2AX is suppressed by olaparib treatment (1 µM, 1 hour). 0.1 % DMSO in medium for 1 hour as mock. The samples were examined by IP and Western blotting. (E) PARP1, but not PARP2, mediates the ADP-ribosylation on H2AX. Wild type (WT) cells, PARP1-null cells or PARP2-null cells were treated with H2O2.
Figure 6Of the three males analyzed, one had XYY sex chromosomes. No abnormalities were found in autosomes in these mice.
Fig.Figure 1A, A phylogenetic tree of 161 different HOX sequences was calculated. HOXs were aligned with 100 iterations with clustal omega. Afterwards the sequences were trimmed by trimAL with gap threshold 0.8 and conservation percentage of 70%. The tree was calculated with PhyML. Akaike Information Criterion, SPR, 200 bootstrap was used. Visualization was done in iTOL. Within the two fungal clades two lichen-derived sequences are shaded in dark blue. B, Alignment of the heme-binding region of several HOs. The heme coordinating histidine is indicated with a star. HoxB lacks this histidine, like HO-2 from A. thaliana.
A.Figure 7A. Confocal imaging analysis depicting mTOR puncta (green) formation on actin filaments (red) in COS-7 cells transiently expressing YFP-mTOR in response to AA stimulation in the presence or absence of latrunculin B (LA-B, 100 nM). Actin filaments were stained using BODIPY™ 558/568-Phalloidin. Arrows indicated the association of mTOR with actin filaments. Scale bar, 5 μm. B. Immunostaining of endogenous mTOR and LAMP1 in C2C12 cells under amino acids starvation (-AA), or in response to AA stimulation (+AA) in the presence or absence of LA-B (100 nM). Scale bar, 20 μm. C. Western blot analysis of mTORC1 activity in C2C12 cells in CM, in response to nutrient starvation and AA stimulation in the presence or absence of LA-B (100 nM). D. Co-IP analysis of the interaction of Aster-C with COPA and MYH10 in the presence or absence of LA-B (100 nM) or cytochalasin D (Cyto-D, 250 nM) in HEK293T cells transiently expressing FLAG-Aster-C. Anti-FLAG antibody was used for immunoprecipitation.
Figure 1Neurosphere assays were performed using mouse E14.5 primary neural progenitors transduced with a retroviral vector expressing Ttyh1 XTT assays were performed using mouse E14.5 primary neural progenitors transduced with a retroviral vector expressing Ttyh1 Neurosphere assays were performed using mouse E14.5 primary neural progenitors transduced with a short hairpin RNA specific to Ttyh1 (shTtyh1) XTT assays were performed using mouse E14.5 primary neural progenitors transduced with a short hairpin RNA specific to Ttyh1 (shTtyh1) Ttyh1-expressing cells in E15.5 embryonic brains that were intraventricularly electroporated at E13.5 were immunostained using an anti-GFP primary (reporter gene) and Alexa Fluor 488-conjugated secondary antibodies. GFP immunofluorescence (green) was merged with DAPI-counterstained images (blue). VZ, ventricular zone; SVZ, subventricular zone; IZ, intermediate zone; CP, cortical plate. Scale bar: 100 μm. Quantification of (E) Double-immunolabeling of E15.5 brain sections electroporated in utero with Ttyh1-expressing plasmid at E13.5 using anti-GFP (green) and Sox2 (red) antibodies, and Alexa Fluor 488- and 555-conjugated secondary antibodies. Scale bar: 50 μm. Double-immunolabeling of E15.5 brain sections electroporated in utero with Ttyh1-expressing plasmid at E13.5 using anti-GFP (green) and Sox2 (red) antibodies, and Alexa Fluor 488- and 555-conjugated secondary antibodies. Scale bar: 50 μm. Quantification of (G) (n = 3). Immunolabeling of E14.5 brain sections electroporated in utero with shTtyh1 alone or in combination with a shTtyh1-resistant Ttyh1 (Ttyh1res) expression vector at E13.5 using anti-GFP and Alexa Fluor 488-conjugated secondary antibodies. The DAPI nuclear counterstain is shown in blue. Scale bar: 100 μm. Quantification of (I)
Screen of D.Fig 2A) Outline of the RNAi screen in primary cultured muscles B) Results of RNAi knockdown screen on autophagic vesicle area/primary muscle cell area. Y-axis is the strictly standardized mean difference (SSMD) scores for each amplicon tested (X-axis). C) GO term enrichment (biological process) of human orthologs hits. Scores on pie chart indicate the log10 p-value of enrichment. D) Hits mapped onto the 187 human genes used as the basis for screening in D. melanogaster. Protein-protein interactions were identified from the set of 409 proteins identified in mammalian cells[16]. For gene knockdowns that inhibited autophagy, dark red indicates that two amplicons had a score < -0.5, while light red indicates that only one amplicon had a significant SSMD score, but that it was < -1. For gene knockdowns that increased autophagy, dark blue indicates that two amplicons had an SSMD score > 0.5, while light blue indicates that only one amplicon had a significant SSMD score, but that it was > 1. (E) At least one amplicon scored as a hit for each of the core autophagy genes tested, with the exception of Atg8, which is our marker for autophagy and is being overexpressed with Dmef2-Gal4, and Atg4.