EMBO/sd-character-level-ner huggingface dataset:
Figure 5(A) Overview of the contact interface. The thumbnail on top indicates the orientation. (B-E) Zoom views on the 40S head-to-head contact site (B), the 40S platform-to-platform contact site (C), the 40S body-to-body contact site (D) and the 60S-to-40S contact site (E). In (D), nucleotides missing in the model at the tip of ES6c are indicated by a dashed line. (F) Location of uS3 (K212) and uS10 (K6 and K8) ubiquitination sites. All ubiquitination sites are in the close spatial vicinity highlighted with red spheres. RACK1 proteins from both the leading and the colliding ribosome form the major head-to-head contact bringing together both C-terminal tails of uS3s as well as the N-termini of uS10s. For the uS10 ubiquitination sites, only an approximate position is shown as indicated by dashed lines since the uS10 N-termini containing K6 and K8 are invisible in the structure most likely due to flexibility.
Host transcriptome responses and risk to SARS-CoV-2.Figure 6:Samples were quantified by a range of viral detection methods, including LAMP (Quantifluor), RNA-seq (log10 SARS-CoV-2 % of reads), and qRT-PCR (Ct values) to create a three-tier range of viral load for the positive samples (right) compared to the clinically-annotated negative samples (class, red or grey). (bottom) The differentially expressed genes of COVID+ patients compared to COVID-patients showed up-regulated (orange) genes as well as down-regulated (purple) genes. (b) Up-regulated genes, with boxplots across all samples, include IFI6, ACE2, SHFL, HERC6, IFI27, and IFIT1, based on data from (c), which is the total set of DEGs. The full set is shown in an intersecting heat map, with a core set of up-regulated genes (orange) distinct form the set of down-regulated genes (purple), compared to genes that are not significantly differently expressed (grey) in any comparison (DESeq2, q-value <0.01, |logFC| >0.58). (d) Significantly different gene ontology (GO) pathways between COVID-POS and COVID-NEG patients include interferon response and host response to infection, as well as some ion and heme transport mechanisms. (e)Survival curves for requiring mechanical respiration (identified by intubation procedure notes) (e)Survival curves for requiring mechanical respiration (identified by intubation procedure notes) (e) and mortality (f). Patients with a history of ACE inhibitor exposure were more likely to require intubation (HR=2.63 95%CI 2.01-3.43, p=1.22E-12; (e) and less likely to survive (HR=1.68 95%CI: 1.22-2.31, p=1.42E-03; (f). Because several individuals were intubated shortly before they first tested positive for SARS-CoV-2 infection, each first positive test was set back by seven days to account for testing delays.
AON-mediated skipping of exon 326 in TTN Ser14450fsX4 induced pluripotent stem cell (iPSC)-derived cardiomyocytes.Figure 2RT-PCR analysis of TTN exon 326 transcripts from DCM cardiomyocytes transiently transfected with 2OMePS-AON1, 2OMePS-AON3, and 2OMePS-AON1 + 3. RT-PCR analysis (left) and representative direct sequencing (right) of TTN exon 326 transcripts from DCM cardiomyocytes infected with the U7snRNA-TTNAONs-IRES-GFP lentiviral vector carrying the AON1 and 3 sequences (TTN-AON) or with a control vector (U7snRNA-ScrAONs-IRES-GFP). Mass spectrometry-based analysis of titin peptides in cells infected with the U7snRNA-ScrAONs-IRES-GFP (Scr-AON) and U7snRNA-TTNAONs-IRES-GFP (TTN-AON) vectors. Unsupervised hierarchical clustering identified a cluster significantly enriched in peptides mapping to exon 326 that was down-regulated in DCM Scr-AON cardiomyocytes compared to CTR Scr-AON cardiomyocytes (n = 3, P = 9.03E−8, Fisher's exact test, FDR = 0.04, top). Down-regulation of exon 326 was also detected in DCM TTN-AON cells when compared to DCM Scr-AON cells (n = 3, P = 0.02, Fisher's exact test, bottom).
Overexpression of TBK1 or TRIF induces ACE2 expression.Figure 3. Overexpression of TBK1 or TRIF induces ACE2 expression.TBK1 is an essential activator of RNA-sensing pathway. HEK293 cells were cultured in 24-well plates. 24 hrs later, plasmids as shown above were transfected into HEK293 cells. 36 hrs after transfection, total RNA was isolation for subsequent RT-qPCR analysis. Results in each panel are representative of three independent experiments.
The combined functions of Jmjd2a and Jmjd2c are essential for early embryonic development.Figure 3A-B. 2ac ESCs expressing GFP were cultured in the absence or presence of OHT and subsequently used for morula injections. (A) Average volume of the GFP-positive area in chimeric embryos at 24 and 72 hrs after morula injection. Number of embryos used for quantification: Ctrl 24h n=18; +OHT 24h n=15; Ctrl 72h n=5; +OHT 72h n=5. Data are presented as mean ± SD. (B) Representative images of chimeric embryos. The white bars indicate a length of 32 µm. Relative intensities of the GFP signal are indicated for each image. C-D. Jmjd2a(+/-); Jmjd2c(+/-) mice were inter-crossed. The number of (C) pups alive at weaning or (D) embryos recovered at E6.5 is presented. P values were calculated using exact binomial test with the most conservative estimate of expected (-/-;-/-) embryos (6.25 %, assuming no linkage between the Jmjd2a and Jmjd2cloci even though they are located on the same chromosome).
Model of RsaI regulation networks in Staphylococcus aureus.Figure 6In the presence of glucose or glucose 6-phosphate (left panel), the expression of RsaI is inhibited, in contrast to RsaG. In the absence of glucose or when glucose is metabolized (right panel), repression of RsaI is alleviated to regulate its RNA targets. In blue, are the transcriptional protein regulators, and in red the regulatory sRNAs. Grey arrows represent functional links, black arrows are for activation, bars for repression. Red lines corresponded to post-transcriptional regulation and black lines to transcriptional regulation. Dotted lines represented the regulatory events for which the regulation is not yet demonstrated. A schematic view of the post-transcriptional icaR mRNA regulation is represented in the insert. The 3'UTR of icaR contains an anti-Shine and Dalgarno (anti-SD) sequence able to bind the SD sequence in the 5'UTR The CU-rich unpaired sequence of RsaI (in red) binds to the 3'UTR of icaR mRNA downstream of the anti-SD, and represses the translation indirectly either by stabilizing the interaction between the two UTRs or by preventing the action of trans-acting activators (protein or RNA).
Figure 8Schematic illustration of the strategy to generate miR-27 and miR-196 knockout embryos. (C) Immunostaining at cervical spinal cord sections reveals Hoxa5 expansion into the MNs of cervical C6/7 segments of miR-23~27~24 double KO (DKO) mice. miR-23a~27a~24-2+/-;miR-23b~27b~24-1-/- mice were used as a control (ctrl). (E) Conversely, Hoxc8 is shifted into the MNs of cervical C5 segments of both miR-196a2/b DKO and miR-196a1/a2/b triple knockout (TKO) embryos. Age-matched wild type embryos were used as controls. Scale bar represents 50 μm. White dash lines demarcate the postmitotoic MN domain (D, F) Quantifications of Hoxa5on, Hoxc8on, and Hoxa5on Hoxc8on cells in the cervical spinal cord of control and knockout embryos (mean ± SD, N=3 embryos, *p < 0.01, Student's t-tests ). Summary of the Hox phenotypes in the miRNA mutants. Yellow squares represent the Hoxa5onHoxc8 on cells.
Figure 3(A) Schematic diagram showing reporter constructs used. The 18-bp PBS sequence was cloned upstream of the HERVK14C LTR promoter (which is identical in all vectors) in an antisense orientation. (B) NTERA-2 cells were transduced with either an empty vector (WT) or the same vector containing an shRNA against KAP1 (KD) prior to puromycin selection and transduction with increasing doses of GFP reporter vectors. GFP expression was analysed 72 hours post reporter transduction. A representative experiment of 2 experiments is shown. Two-tailed unpaired t test p-values: PBS-LTR-GFP: 0.0148; PBSChr15-LTR-GFP: 0.0377 (C) The same as (B) except that here KAP1 wildtype (WT) and knockout (KO) 293T cells were used. P-values: PBS-LTR-GFP: 0.0044; PBSChr15-LTR-GFP: 0.0077. (D) PBMCs were transduced with increasing doses of GFP reporter vectors (vectors were normalized to the same number of infectious units after titering them on permissive cells), left plot. Vectors were integrated at similar levels as measured by GFP Taqman qPCR, right plot. A 293T cell line with a single vector copy integrant (PGK-GFP) was used as a control to estimate the absolute copy numbers. A representative experiment of 3 experiments is shown here. Two-tailed unpaired t test p-value 0.0288 (dose 3). Error bars show SD. (E) The expression of 340 KZNFs was assessed in multiple cell types using public mRNA-sequencing data and Venn diagrams show the overlap in expression profiles. KZNFs were considered to be expressed in a particular cell type if their expression value was >0.5 RPKM in all replicates.
Physiological renal aging is characterized by glomerulosclerosis, podocyte loss and glomerular endothelial senescence.Figure 1A: Morphology (PAS staining, upper panels) and quantification of glomerular lesions (lower panel) of kidneys from young and aged mice. Original magnification X400. Scale bar = 20 μm. n = 6 for young and old mice, respectively. B: WT1 immunohistochemistry (upper panels) and quantification of WT1-positive glomerular cells (lower panel) in kidneys from young and aged mice. Original magnification X400. Scale bar = 20 μm. n = 6 for young and old mice, respectively. C: TUNEL assay (upper panels) and quantification of TUNEL-positive tubular cells (upper panel) in glomeruli from young and aged mice. Panels are representative images of 6 young and old mice, respectively. Scale bar = 20 μm. D: Senescence-associated β-galactosidase staining (upper panels) and quantification of β-galactosidase-positive glomeruli (lower panel) in kidneys from young and aged mice. Original magnification X400. Scale bar = 20 μm. Panels are representative images of 4 young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice. E: p21/griffonia simplicifolia/nephrin coimmunostaining in kidneys from young and aged mice (left panels) and quantification (right panel) of p21-positive endothelial cells per glomeruli. Original magnification X630. Scale bar = 10 μm. Panels are representative images of 6 young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice. F: 53BP1/CD34 co-immunostaining in kidneys from young and aged mice (left panels) and quantification (right panels) of 53BP1 foci per glomerular endothelial cell. Original magnification X630. Scale bar = 10 μm. Panels are representative images of 6 young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice. G: p16 mRNA expression in whole kidney from young and old mice. n = 6 for young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice. H: mRNA expression of SASP components in kidneys from young and aged mice. n = 6 for young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice. I: PAI-1 immunohistochemistry (left panels) and quantification of PAI-1-positive glomeruli (right panel) in kidneys from young and aged mice. Original magnification X400. Scale bar = 20 μm. n = 5 for young and old mice, respectively. Data information: Data are means ± SEM. Statistical analysis: t-student test: young versus old mice.
PERK knockdown rescues mitochondrial morphology and excessive ROS production in Mfn2 KO cells.Figure 8(A) Representative confocal images of mitochondrial morphology in scrambled (Scr) and PERK KD Mfn2 KO cells stained with MitoTracker Green. (B) Mitochondrial morphology quantification. Data are mean±s.e.m. (n=3; 100 cells were analyzed per experiment and group). *P0.05 versus Scr group. (C, D) Representative confocal images of mitochondrial morphology in scrambled (Scr) and PERK KD WT cells (C) or scrambled (Scr) and PERK KD Mfn1 KO cells (D) stained with MitoTracker Green. (E) Representative confocal images of mitochondrial morphology in Mfn2 KO cells treated with 1 μM TUDCA or 10 mM 4‐phenyl butyric acid for 6 h and stained with MitoTracker Green. (F) Flow‐cytometry quantification of ROS levels in Scr and PERK KD WT and Mfn2 KO cells (G) or Scr and PERK KD WT and Mfn1 cells using DHR1,2,3. Data are mean±s.e.m. (n=4). *P0.05 versus WT group, #P0.05 versus Scr group. Scale bars: 10 μm.
a, RAW 264.figf2a, RAW 264.7macrophages infected for 4 or 8 h were analysed by TEM. Shown are spacious vacuoles (SLAPs) containing multiple bacteria. The arrow indicates septum of dividing bacteria. Scale bars, 0.5 µm. b, The arrow indicates a LAMP1+ SLAP colocalizing with green fluorescent protein (GFP)-LC3 in cells infected for 4 h.The percentage of GFP-LC3+ (c) d, The arrowhead indicates a LAMP1+ SLAP devoid of cathepsin D in cells infected for 4 h. Scale bars, 5 µm.The percentage of GFP-LC3+ (c) or cathepsin D+ (e) f, GFP-LC3-transfected macrophages were infected with wild-type or D actA bacteria. Where indicated, chloramphenicol (CM) was added to the media at 3 h post infection. The number of bacteria per SLAP was quantified. Brackets indicate significant differences, and corresponding P values are shown. g, Macrophages were infected with wild-type bacteria for 7 h, pulsed with BrdU for 1 h, and stained for LAMP1 (red), bacteria (blue) and BrdU (green). Magnified images and the arrow indicate SLAPs containing actively replicating bacteria (BrdU+). h, The percentage of BrdU+ bacteria in SLAPs, compared to bacteria and PFA-killed bacteria, was quantified as in c.
– Model.Figure 8We propose the following model: Jmjd2a and Jmjd2c are both recruited through their double Tudor domains to H3K4me3 marked nucleosomes, where they continuously and redundantly prevent accumulation of H3K9me3 and H3K36me3. In the absence of Jmjd2a/c catalytic activity, substantial increases in H3K9me3 levels at specific loci impair gene expression, which perturb the transcriptional programme required for embryonic stem cell identity, proliferation and embryonic development.
Impact of NSMCE2 deletion in embryos and adult miceIntrauterine dwarfism observed upon NSMCE2 deletion on 17.Figure 6Intrauterine dwarfism observed upon NSMCE2 deletion on 17.5 dpc embryos. Pregnant females were treated at 14.5 dpc for 3 days with intraperitoneal injections of 4‐OHT. The image represents the difference in size observed between Nsmce2+/+ and Nsmce2lox/lox embryos carrying the UQ.CreERT2 transgene (Nsmce2+/+ and Nsmce2lox/lox, from now on). Representative picture of Nsmce2+/+ and Nsmce2lox/lox animals fed for 40 weeks with a 4‐OHT‐containing diet (see also Movies EV1 and EV2). Images illustrating the presence of altered pigmentation problems that arise on Nsmce2lox/lox mice. Percentage of fat against total body mass on Nsmce2+/+ and Nsmce2lox/lox animals. ***P 0.001. White bloodcell counts (WBC) from Nsmce2+/+ and Nsmce2lox/lox animals. ***P 0.001. Percentage of γH2AX‐positive micronuclei found on the intestinal epithelia of Nsmce2+/+ and Nsmce2lox/lox animals (see Appendix Fig S11). Data are representative of three independent experiments. Error bars indicate SD. *P 0.05.
Figure 10Model of UBR7 function. In the absence of UBR7, sNASP-bound H3K4me3 is not deposited, and total non-nucleosomal H3 and sNASP-bound H3K4me3 accumulate, leading to depleted H3K4me3 at UBR7 binding sites in chromatin.
Figure 4(A) Experimental design to test effects on olfaction. (B) Scheme of the go/no-go odor discrimination task. Mice introduce their head in the sampling port breaking the infrared beam (IR). A correct response is scored when mice retract their head in the presence of an unrewarded odor or, alternatively, wait and lick for a rewarded one. See additional information in Appendix. (C) Line graph indicating the proportion of correct responses (performance) for bins of 100 trials each during testing with binary mixtures of concentrated octanols. Discontinuous line indicates the similar 95% plateau performance of 4D- (black) and 4D+ (red) mice. (D) Whiskers box plots of performance (left) and lick frequency (right) during a probe of 200 trials with 1:10 diluted octanols after testing as in (C).
Figure 7WB analysis of detergent-soluble and -insoluble fractions of HeLa and TRIM16KO cells expressing either (A) Flag-p62 probed with Flag or indicated antibodies. L.E, Low exposure; H.E, High Exposure. Densitometric analysis of WB's normalized with α-Tubulin or Lamin-B1. WB analysis of detergent-soluble and -insoluble fractions of HeLa and TRIM16KO cells expressing either (C) GFP-polyQ74 probed with or GFP or indicated antibodies. L.E, Low exposure; H.E, High Exposure. Densitometric analysis of WB's normalized with α-Tubulin or Lamin-B1. (E) Confocal images of GFP-TRIM16 expressing HeLa cells, untreated or treated with MG132 (10 µM, 4h) and/or Bafilomycin A1 (300 nM, 3h) and IF analysis is performed with antibodies as indicated. Right panel graphs: fluorescence intensity line tracing corresponding to a white line in zoom panel. Scale bar: 10 µm. (F) The graph shows the percentage of cells with TRIM16-Ub or TRIM16-Ub-p62 co-localized dots/aggregates. Data from ≥ 10 microscopic fields, n=2, mean ±SD. (G) Representative confocal images of GFP-TRIM16 expressing HeLa cells, untreated or treated with MG132 (10 µM, 4h) and/or Bafilomycin A1 (300 nM, 3h) and IF analysis is performed with antibodies as indicated. Right panel graphs: fluorescence intensity line tracing corresponding to a white line in zoom panel. Scale bar: 10 µm. (H) Co-IP analysis of the interaction between two differently tagged TRIM16 variants. (I) WB analysis of detergent-soluble and -insoluble DSS-cross-linked fractions of HeLa and TRIM16KO cells, untreated or treated with MG132 (10 µM, 4h) and probed with indicated antibodies. (J) Co-IP analysis of the interaction between Flag-tagged TRIM16 and Myc-tagged TRIM16 full length and its domain deletion proteins.
Figure 5A-C Male cynomolgus monkeys were treated with vehicle control (n=2), AT845 (n=3) at 6×1013, 2×1014, or 5×1014 vg/kg, or Cyno-AT845 (n=3) at 2×1014 vg/kg and followed for approximately 12 weeks. (A) Anti-GAA antibody titer, (B) cardiac troponin I (cTnI), and (C) N-terminal pro b-type natriuretic peptide (BNP). Bars show mean and SEM.
Figure 5A) Volcano plot comparing the number of transposon insertions per gene of all 24 rewired libraries and two wild-type (wt) libraries. Genes that are significantly (p-value < 0.05) required (red, log2(fold change) < -1.5; blue, log2(fold change) < -1) or dispensable (green, log2(fold change > 2)) in the rewired libraries are highlighted. Genes depicted in grey are essential due to differential growth requirements in the preparation of the two wt libraries compared to the rewired strains, or correspond to genes deleted in the rewired strains. B) Requirement for mitochondrial lipid transport and biosynthesis genes in rewired libraries. Left panel, schematic depicting PE and cardiolipin (CL) synthesis in mitochondria. The inner mitochondrial putative lipid transporter Mdm31 is depicted in yellow. Grey arrows indicate the need for lipid transport from the ER or other organelles to mitochondria and transport between the MOM and MIM. Right panel, transposon numbers (normalized to wt libraries) for the indicated (set of) libraries for MDM31, PGS1, and CRD1.
Flagellar sub-complexes in P.Figure 3Slices through electron cryo-tomograms showing fully-assembled motors without the hook and filament. The dashed-yellow circles indicate the IM sub-complex. Schematic representation of the P. aeruginosa motors lacking the hook and filament shown in (A-C). Slices through electron cryo-tomograms showing fully-assembled motors with the hook and lacking the filament. Schematic representation of the motors with the hook shown in (E-G). Slices through electron cryo-tomograms of intact P. aeruginosa ∆flgI cells showing the presence of the inner-membrane sub-complex with the rod. Schematic representation of the inner-membrane sub-complex with the rod shown in (I-K). Slices through electron cryo-tomogram of lysed P. aeruginosa ∆flgI cells showing the presence of the sub-complex constituting the MS-ring and the rod. Schematic representation of the sub-complex described in (M-O). A slice through an electron cryo-tomogram of a P. aeruginosa ∆flgG cell highlighting the presence of the inner-membrane sub-complex. Schematic representation of the inner-membrane sub-complex shown in (Q).
Intracellular redox status governs activation of AosRa.Figure 6Multiple sequence alignment of AosR from various mycobacterial species. CxxxC motif present within the N terminus extension is highlighted using a blue box. * perfect alignment : strong similarlity and . represents weak similarility. Secondary structure model of AosR predicted by I-Tasser Web server. Early log-phase cultures of indicated strains were subjected to 50 µM of CHP for 24 h and CFUs were enumerated (mean±SEM; n=3). Control represents untreated cells. 1 µM AosR was treated with various ratios of oxidized to reduced DTT (ox:red DTT- 3:1, 2:2, 1:3), or only with 4 µM reduced or oxidized DTT. mBBr was added to the reaction mixture and the fluorescence intensity was measured from 430-600 nm upon excitation at 390 nm wavelength. Reaction mixture without any protein was used as blank (mBBr). Each spectrum represents an average of three individual scans. Early log-phase cultures of indicated strains were subjected to 50 µM of CHP for 24 h and CFUs were enumerated (mean ±SEM; n=3). Control represents untreated cells. pΦ from Balb/C were infected with indicated strains and bacterial viability was monitored 0 and 96 h p.i. Data is presented as mean CFU log10/ml ± SEM and is representative of two biologically independent experiments, each performed in triplicates (n=3). BLI sensorgram illustrating relative binding affinities of 800nM His-AosR and His-AosRAxxxA to immobilized His-SigH under oxidizing conditions. Msm::FLAG-SigH, Msm::FLAG-SigH-AosR-HA and Msm::FLAG-SigH-AosRAxxxA-HA were either subjected to none or 50 µM of CHP for 3 h followed by cross-linking. 1 mg WCL was used to immunoprecipitate FLAG-SigH and 1/10th IP was probed with α-FLAG and 9/10th IP with α-HA. 50 µg WCLs were probed with α-FLAG, α-HA and α-SigA as controls.
Model of AP-3 vesicle tethering and fusion at the vacuole.Figure 8AP-3 vesicles require an assembled coat to interact with vacuole-localized HOPS, and bind to Vps41. Interaction with vesicle SNAREs capture AP-3 vesicles stably, and allow partial uncoating via the Arf GAP Age2. SNARE and HOPS interactions then drive fusion with the vacuole.
Characterization of epigenetic and genetic features of agonist‐liganded ARBE locationsAggregated sequencing tag distribution of AR ChIP‐exo and H3K4me2 MNase ChIP‐seq around the four precisely defined ARBEs.Figure 4A Aggregated sequencing tag distribution of ARChIP‐exo and H3K4me2 MNaseChIP‐seq around the four precisely defined ARBEs. ChIP‐exo density plot is shown as forward (blue) and reverse (red) strands, respectively. H3K4me2 signal is shown in green. The window indicates ± 500 bp regions from the ARBE motif (0). B Partitional clustering of the 4 types of ARBE locations based on dynamic signal shifting of H3K4me2 affected by DHT treatment. C Venn diagram of DHS sites and ARBEs. Right panel shows DNase‐seq tag distribution around ARBEs within ± 1 kb. D Profile of all clusters of each type of ARBE associated with FOXA1 motifs. E Conservation profile of the four types of ARBEs calculated by phyloP. F SNP frequency comparison between each type of ARBE and whole‐genome control. **P 1E‐8, *P 1E‐5.