EMBO/sd-character-level-ner huggingface dataset:
Fig.Figure 6(A) A diagram of eye-specific segregation assay at P30. (B) CTB-labeled dLGN shows reduced eye-segregation at P30 in CKO mice. The left column shows contralateral dLGN labeled with CTB488 (green), and the middle one is ipsilateral dLGN with CTB647 (magenta). The right column represents the dLGN pseudocolored according to the R-value for each pixel (R = log(Fipsi/Fcontra)). (C) A histogram distribution chart of R-value for all pixels within dLGN represents the degree of eye-specific segregation. When R is 0, it means equal ipsilateral and contralateral fluorescence intensity at a pixel. A greater R-value means a bigger difference of ipsi-to-contraleteral fluorescence intensity. The narrower distribution of CKO in the inset indicates reduced segregation. (D) The variance of R distributions in P30 control and CKO mice. N = 4 (Ctrl), N = 6 (CKO), p = 0.004, mean ± SD. (E) A schematic diagram of electrophysiological recording in a parasagittal dLGN. (F) Maximal NMDAR mediated currents measured in the dLGN of P28~P34 mice, p = 0.03, N = 14 (Ctrl), 23 (CKO) cells from 5, 7 mice, respectively. Mean ± SEM. (G) Western blot of NMDAR1 using microdissected dLGN tissue from P30 mice. (H) Quantification of NMDAR1 expression in CKO mice and control. (I) Maximal AMPAR mediated currents measured in the dLGN of P28~P34 mice. P=0.302, N = 13 (Ctrl), 17 (CKO) cells from 5, 7 mice, respectively. Mean ± SEM. (J) Western blot of GluR1 with microdissected P30 dLGN tissue. (K) Quantification of GluR1 expression in CKO mice and controls.
Figure 3A Quantification of IRF5 and IFNB1 mRNA expression in peripheral blood mononuclear cells of non-diabetic (ND) and type 2 diabetic (T2D) COVID-19 patients (A). B Histograms of IRF5 expression on different populations analysed by flow cytometry on venous blood samples. C IRF5 median fluorescence intensity (MFI) in monocytes of ND and T2D patients with COVID-19. D IRF5 expression overlaid onto monocyte phenotypic gating. E IRF5 expression (MFI) in monocyte subtypes from ND and T2D COVID-19 patients. F HLA-DR and IRF5 expression in monocytes from COVID-19 patients. G IRF5 expression in monocytes of ND or T2D COVID-19 patients admitted to intensive care unit (ICU) or treated exclusively in general wards (Gen) . H IRF5 expression in monocytes of ND or T2D COVID-19 patients admitted ICU or treated exclusively in Gen.
Figure 2PC9 cells (3X106/mouse) were subcutaneously implanted in the flanks of CD1-nu/nu mice. When tumors became palpable, mice were randomized in groups of 5-9 animals and treated for 90 days (grey areas) with 2XmAbs (cetuximab plus trastuzumab, 0.2 mg/mouse/injection), once every three days, or with erlotinib (50 mg/kg/day), once per day. Alternatively, mice were treated with combinations of erlotinib (50, 20, 10, 5 or 1 mg/kg) and the two monoclonal antibodies. Following 60 days of treatment reduced the frequency of erlotinib administration to once every other day (underneath dotted line). Tumor volumes (A) are shown. Mice were euthanized when tumor size reached 1,500 mm3. PC9 cells (3X106/mouse) were subcutaneously implanted in the flanks of CD1-nu/nu mice. When tumors became palpable, mice were randomized in groups of 5-9 animals and treated for 90 days (grey areas) with 2XmAbs (cetuximab plus trastuzumab, 0.2 mg/mouse/injection), once every three days, or with erlotinib (50 mg/kg/day), once per day. Alternatively, mice were treated with combinations of erlotinib (50, 20, 10, 5 or 1 mg/kg) and the two monoclonal antibodies. Following 60 days of treatment reduced the frequency of erlotinib administration to once every other day (underneath dotted line). animal survival (B) are shown. Mice were euthanized when tumor size reached 1,500 mm3. (C) Statistical analysis of tumor volumes corresponding to the last measurement for each mouse was performed using one-way ANOVA followed by Tukey's multiple comparison test. (D) Shown are tumor volumes of individual mice of each group. Note that each animal is represented by a different color. The respective numbers of tumor-free mice are indicated. The grey areas represent treatment phases and they are followed by drug holidays (blank).
Figure 1A) Partial amino acid sequences of the hMPV F (blue) and hRSV F(red) antigenic site II (Lopez et al., 1998;McLellan et al., 2011b;Toiron et al., 1996). Partial sequences of the F-415 and F-416 chimeras are color coded to indicate the origin of their antigenic site II residues. Amino acids shared by hMPV F and hRSV F are colored purple. The remaining sequences of F-415 and F-416 are derived from hMPV F. B) Surface representation of the hMPV F structure in the postfusion conformation (Mas et al., 2016). One of the protomers is shown as a blue ribbon. Antigenic site II is magnified and colored as in (A) for the F-415 and F-416 chimeras. C) ELISA binding results of mAbs specific for hRSV F (left panels) or hMPV F (right panels) with the proteins indicated at left. mAbs specific of hRSV F bind epitopes of antigenic site II (Mota and 47F) or antigenic site IV (101F). mAs specific of hMPV F bind epitopes of antigenic site II (MF9, MF12, MF14 and MF15) or antigenic site IV (MF16).
53BP1 compartments are more long-lived than MDC1 foci.Figure 2U-2 OS cells were treated with 0.5 Gy of IR, allowed to recover for the indicated time periods, stained for 53BP1 and MDC1, and analyzed by QIBC. 53BP1 foci intensities are plotted against MDC1 foci intensities, and representative images are shown. U-2 OS cells stably expressing GFP-MDC1 or GFP-53BP1 were treated with 1 Gy of IR and analyzed by live cell microscopy at 15 min intervals. Representative images are provided and kinetics of GFP-MDC1 and GFP-53BP1 foci formation and dissolution are shown as single cell tracks. Bold lines represent averages from n=29 for GFP-MDC1 and n=18 for GFP-53BP1 cells.
Tollip and Parkin facilitate TOM20 MDV endocytic trafficking to the lysosome.Figure 8Mitochondrial stress induces the formation of single membrane TOM20 mitochondrial-derived vesicles (MDVs) through a currently undefined mechanism. Following budding, Tollip is essential for MDV transition into an early endosomal compartment followed by the concomitant recruitment of Parkin. Tollip and Parkin work in close association to transfer MDV cargo through the endosomal system, thus requiring both of their function for trafficking onwards to the lysosome. Fusion with endosomal intermediates to facilitate maturation and subsequently fusion with lysosomal compartments is required to mediate turnover of MDV cargo. Constituents such as Tollip and Rab7 are 'recycled' from the lysosome back to endosomal bodies via a retromer-dependent pathway.
Figure 3A Splicing isoforms of the CLK1 pre-mRNA. The retained introns are indicated by red lines. An asterisk indicates the position of the premature termination codon in the nonsense-mediated mRNA decay-targeted isoform. B Time course analysis of the splicing pattern of CLK1 pre-mRNAs in control and HSATIII knockdown (HSATIII KD) cells by semi-quantitative RT-PCR. Arrows indicate the positions of PCR primers. The GAPDH mRNA was used as an internal control. C Quantification of the data shown in (B). Data are shown as the mean±SD (n=3); *p<0.05 (Sidak's multiple comparison test). D Thermal stress-induced expression of HSATIII in CHO (His9) cells. The cells were visualized by HSATIII-FISH (green), and the nuclei were stained with DAPI (blue). Scale bar: 10 μm. E Ectopic HSATIII-induced nSB assembly in CHO (His9) cells. The nSBs (yellow arrowheads) were visualized by HSATIII-FISH and immunofluorescence using an anti-SRSF1 antibody. The nuclei were stained with DAPI. Scale bar: 10 μm. F Time course analysis of the splicing pattern of Chinese hamster Clk1 pre-mRNAs in control (CHO) and CHO (His9) cells by semi-quantitative RT-PCR. Arrows indicate the positions of PCR primers. The GAPDH mRNA was used as an internal control. Time course analysis of the splicing pattern of Chinese hamster Clk1 pre-mRNAs in control (CHO) and CHO (His9) cells by semi-quantitative RT-PCR. Arrows indicate the positions of PCR primers. The GAPDH mRNA was used as an internal control. G Quantification of the data shown in (F). Data are shown as the mean±SD (n=3); *p<0.05 (Sidak's multiple comparison test). H The effect of HSATIII knockdown on pooling of intron-retaining RNAs in control (CHO) and CHO (His9) cells (42°C for 2 h and recovery for 2 h at 37°C). Arrows indicate the positions of PCR primers.
Figure 7Proposed mechanism of ASCO lncRNA action. ASCO hijacks NSR proteins to modulate the population of alternatively spliced transcripts. Additionally, ASCO is recognized by PRP8a and SmD1b, two core components of the spliceosome, conditioning the SmD1b/PRP8a-dependent transcriptome diversity in response to flagellin.
a) Growth of TbMCU-KO BSF in the absence (black line) or presence (red line) of 1 μg ml−1 tetracycline for the indicated number of days.f5(a) Growth of TbMCU-KO BSF in the absence (black line) or presence (red line) of 1 μg ml−1 tetracycline for the indicated number of days. Addition of 10 mM threonine to the medium (green line) partially rescued the mutant BSF trypanosomes but had no effect on +Tet cells (yellow line; means±s.d., n=3, **P0.001, Student's t-test). (b) Southern blot analysis of the BSF conditional KOs. Genomic DNA from the T. brucei SM parental strain (+/+), single- (+/−) or double-allele (−/−) KO cells. (c) Northern blot analysis of wild-type (WT) and TbMCU-KO BSF cultured in the presence (+Tet) or absence (−Tet) of tetracycline for 2 days. Tubulin is shown as a loading control (bottom panel). (d) Western blot analysis of total cell lysates. Proteins from BSF trypanosomes cultured in the presence (+Tet) or absence (−Tet) of tetracycline were detected using anti-HA antibody. TbVDAC was used as a loading control. (e) Immunofluorescence analysis of control (upper panels) and TbMCU-KO (lower panels) trypanosomes. TbMCU co-localized with MitoTracker (MT) in the control parasites (+Tet; PCC=0.808). Scale bar, 10 μm. (f) Conditional TbMCU-KO BSF trypanosomes were grown in the presence (+Tet) or absence (−Tet) of tetracycline for 2 days. BSF trypanosomes (2 × 108 cells) were incubated as in Fig. 2e. Multiple pulses of CaCl2 (arrowheads) were added to a final concentration of 20 μM. A representative trace (red or black) of Ca2+ uptake from one of three independent experiments is shown. (g) Representative traces of mitochondrial membrane potential of digitonin-permeabilized BSF trypanosomes grown in the presence (+Tet) or absence (−Tet) of tetracycline. The reactions were incubated as in Fig. 3c. CaCl2 (50 μM), EGTA (200 μM) and FCCP (10 μM) were added where indicated. (h,i) Representative traces of mitochondrial membrane potential of digitonin-permeabilized BSFtrypanosomes grown in the presence (+Tet) or absence (−Tet) of tetracycline. The reactions were incubated as in Fig. 3c. CaCl2 25, 50 and 100 μM CaCl2) or FCCP (i) to +Tet and −Tet BSFtrypanosomes (means±s.d., n=3, **P0.001, Student's t-test).
Figure 6A. Representative traces of Ca2+-currents and 4-AP insensitive K+-currents evoked by step depolarizations (from −50 mV to +10 mV in 10 mV increments), recorded from the calyx terminals in acute slices from littermate control and Nrxn123 TKO mice at P12-P14. B. Same as (A) but after addition of 200 nM iberiotoxin (IbTx) by perfusion. C. Representative traces of presynaptic BK currents , which are calculated by subtracting currents shown in (B) from currents shown in (A). D. Summary graphs of the capacitance, Ca2+-current density, and BK-current density.
Figure 4A. Diagram showing 7 of 10 key glycolytic enzymes that were identified as HAT1 succinylation targets (red boxes) in the succinylation quantitative proteomics. B. Bar graphs depicting the relative ratio of succinylation in HAT1 KO versus WT of the 7 key enzymes in the glycolysis pathway depicted in (A). N = 3 biological replicates. Data were presented as mean ± SD. C. The diagram showed the MS/MS spectra of PGAM1 K99succ peptide for its identification and quantification. The b and y represented the fragment ions of the N and C termini in peptide backbone, respectively. m/z, mass-to-charge ratio. D. The decrease of glucose and increase of lactate in culture medium were measured by ELISA assays in HepG2 cells, HAT1 KO HepG2 cells, and HAT1 KO HepG2 cells reconstituted with either wild type HAT1 or mutant HAT1 (T188A). N = 3 biological replicates. Data are presented as mean ± SD. Student's t-test, **P < 0.01. E, F. The relative amounts of indicated metabolites were quantified by ELISA assays in HepG2 cells, HAT1 KO HepG2 cells, and HAT1 KO HepG2 cells reconstituted with either wildtype HAT1 or mutant HAT1 (T188A). N = 3 biological replicates. Data are presented as mean ± SD. Student's t-test, **P < 0.01; ns, no significance.
Inhibition of autophagy by full‐length TAB2 and TAB3 but induction by their C‐terminal fragments.Figure 5(A) Effects of full‐length TAB2 and TAB3 or their deletion mutants (as in Figure 1C) on autophagy. HeLa cells stably expressing GFP-LC3 were transfected with pcDNA3.1 (empty vector) or with plasmids encoding the indicated TAB2 and TAB3 variants for 24 h, then driven into autophagy by starvation or by the administration of 1 μM rapamycin or 30 μM pifithrin α (PFTα) for 4 h. Finally, the frequency (mean±s.d., n=3) of cells with >5 GFP-LC3+cytosolic puncta (GFP-LC3VAC cells) was assessed (*P0.01 versus control cells transfected with the same plasmid; #P0.01 versus pcDNA3.1‐transfected cells treated with the same pro‐autophagic trigger). (B) U2OS cells stably expressing FYVE-RFP were co‐transfected with pcDNA3.1 or with vectors encoding TAB2C or TAB3C together with a control siRNA (siUNR) or with siRNAs specific for VPS34, Beclin 1 (BCN1) or TAK1 for 24 h, followed by the quantification of cells exhibiting FYVE-RFP+ dots (FYVE-RFP+). Results are mean values±s.d. (n=3; *P0.01 versus siUNR‐, pcDNA3.1‐transfected cells). (C) Inhibition of the interaction between endogenous TAB2, TAB3 and BCN1 by C‐terminal fragments of TAB2 and TAB3. Forty‐eight hours after transfection with pcDNA3.1 or plasmids coding for the indicated proteins, cells were lysed, TAB2 or TAB3 was immunoprecipitated and BCN1 was immunodetected. GAPDH levels were monitored to ensure equal loading. This experiment has been done three times, yielding comparable results. (D) Mechanisms of autophagy induction by the Beclin‐binding domain (BBD)‐containing C‐terminal fragments of TAB2 and TAB3. HeLa cells were transfected with pcDNA3.1, TAB2C‐ or TAB3C‐encoding plasmids in combination with the indicated siRNAs for 24 h, followed by the quantification of GFP-LC3VAC cells (mean values±s.d., n=3; *P0.01 versus siUNR‐, pcDNA3.1‐transfected cells).
α to modulate adipocyte metabolic status.Figure 4Venn diagram demonstrating the significant enrichment of QKI-mediated change genes in the set of QKI binding genes determined by RIP-seq experiment. Only 30 genes identified by microarray analysis were also QKI binding targets. Schematic diagram of search strategy to identify genes, which contained QRE motif sites and involved in controlling adipose thermogenic metabolism. The following publicly available datasets were used for the comparisons: brown versus white adipose tissues (WAT) (NCBI GEO: GSE51080), BAT following cold exposure (NCBI GEO: GSE40486) and WAT following cold exposure (NCBI GEO: GSE51080). The protein levels of PGC1α and QKI in siRNA-mediated QKI knockdown differentiated cell, and the quantification graph was shown on the right. (n=3 biological replicates) Immunostaining of PGC1α and UCP1 in NC, Si-QKI 1, and Si-QKI 2 adipocytes. (Scale bar represents 20 μm). The relative mRNA levels of genes related to thermogenesis in adipocytes treated with NC, QKI siRNA or both QKI and PGC1α siRNA. (n=3 biological replicates) The oxygen consumption rates in adipocytes treated with NC, QKI siRNA or both QKI and PGC1α siRNA. (n=3 biological replicates) Representative pictures of oil red O staining in three adipocyte types: ShScramble+ovCon cells, QKI knockdown cells (ShQKI+ovCon) and QKI knockdown with QKI-5 re-expression cells (ShQKI+ovQKI). The protein levels of PGC1α in these adipocytes, and the quantification graph was shown on the right. (n=3 biological replicates) The relative mRNA levels of genes associated with energy dissipation in ShScramble+ovCon, ShQKI+ovCon and ShQKI+ovQKI differentiated cells. The results represent 3 independent experiments.
In vivo enzyme kinetics of Tmk is highly cooperative and different from that in vitro.Figure 6in vitro activity of purified Thymidylate Kinase (Tmk) as a function of dTMP concentration shows Michaelis-Menten (MM) like kinetics. ATP concentration is saturating at 1mM. The KM of dTMP is 13μM. The error bars represent SD of three technical replicates. For a 10-fold drop in intracellular dTMP concentration in mutant relative to WT (as seen in I91L+W133V mutant), we calculate dTDP levels in mutant (relative to WT) as a function of various assumed intracellular concentrations of dTMP in WT (shown along x-axis), as absolute value of this is not known experimentally, assuming MM kinetics (black line) as shown in panel (A) or Hill kinetics with coefficient of 2.5 (red line) as shown in panel (C). The dotted line corresponds to the experimentally observed dTDP ratio of 0.01 for I91L+W133V mutant. This ratio is realized only for the Hill-like curve. Apparent in vivo activity kinetics of Tmk enzyme using steady state dTMP and dTDP levels obtained from metabolomics. The plot includes data from WT, mutants W133V and I91L+W133V, as well as WT treated with 0.5μg/ml Trimethoprim, obtained at different time points during growth. Data points represent metabolite levels for all individual biological replicates without averaging. The black data points were acquired during growth in the presence of different concentrations of external dTMP (0.25, 0.5, 1, 2 and 5mM), while red points were from conditions with no external dTMP. Both black and red solid lines represent fit to Hill equation. The green points were acquired during growth of WT, W133V and I91L+W133V mutants in the presence of different concentrations of thymidine, which follow the red curve. The inset plot shows the same graph with selected datapoints for I91L+W133V mutant. The cyan circle shows I91L+W133V mutant in the absence of any metabolite supplementation, while red and black points indicate metabolite levels following thymidine and dTMP supplementation respectively. A flow chart summary of the actual chain of events triggered by destabilizing mutations in DHFR that eventually lead to bacterial filamentation, as revealed in this study.
Chorion single cell transcriptomeA.Figure 6A. Scheme of chorion isolation where mesoderm is in green (mG), and the other cells are in grey (mT). B. UMAP (Left) and RNA velocity (Right) of chorion cells where 5 unsupervised clusters were identified. C. UMAP of eGFP, Krt8, Cdh1 and Cdh2. D. Dot plot of specific gene expression in chorion clusters. E. Immunostaining for Cdx2 (n=20). F. Immunostaining for DAPI (cyan, left), Sox2 (middle), and Gata2 (right). Sox2 is primarily expressed in Trophoblast Progenitors and Gata2 in Chorion Ectoderm. G. Immunostaining for Cebpb, detectable in most cells with variable intensity. H. Immunostaining for Fn1 (n=22), Dlk1 (n=8), and Acta2 (n=12), primarily expressed in Chorion Mesenchyme. I. Sections from C57BL/6J wild-type and KtyII-/- LB embryos immunostained for Dlk-1 (n=8 and 4, respectively) and Acta2 (n=6 and 3). Data
NOS Overexpression Primarily Inhibits the JNK1–Bcl-2 Pathway to Impair Autophagy.Figure 6(A-F) Immunoblot analyses with anti-nNOS, anti-iNOS, anti-eNOS, anti-phospho-JNK1, anti-phospho-Bcl-2, anti-phospho-S6K, and anti-phospho-S6 antibodies show that stable HEK293 cell lines overexpressing nNOS (A and D), iNOS-GFP (B and E), or eNOS (C and F) inhibited both the JNK1-Bcl-2 and mTORC1 pathways compared to the HEK293 control cells under basal (FM) (A-C) or starvation (HBSS) (D-F) conditions. Graphical data denote mean ± SEM.
Figure 1(left) Luciferase expression in HEK293 cells driven by deletion constructs of POLG proximal promoter. (right) Luciferase expression with mutated CAAT-boxes in POLG promoter. The error bars indicate standard deviation in 3 biological replicates. AU; arbitrary units. POLG promoter sequence showing predicted CAAT-boxes. Red shows disrupted nucleotides by site-directed mutagenesis in (a). Expression pattern driven by 500 bp Polg proximal promoter in E12.5 mouse embryo. LacZ-positive cell populations in the developing midbrain (black arrows), dorsal root ganglia (grey arrows) and motoneuron progenitors (arrowhead) of the neural tube. Somites show some expression (white arrow). Sectioning planes indicated by red lines. Scale bars 100 µm. Prediction of enhancers in the genomic loci of mtDNA maintenance genes, 100 kb upstream of the analyzed gene, found in human-mouse and human-rat comparisons. EEL score for individual elements: red bars. Protein coding genes upstream from mtDNA maintenance genes are shown with black lines under each locus (picture not in scale). POLG shows three highly conserved elements in a gene-poor region. TWNK shows one distant element, with several genes between the element and the gene, suggesting the element not be a specific regulator for TWNK. Abbreviations: TWNK, Twinkle mtDNA helicase; POLG, DNA polymerase gamma, catalytic subunit; POLG2, DNA polymerase gamma, accessory subunit; SSBP1, single stranded DNA binding protein 1; TFAM, mitochondrial transcription factor A. - (G) POLG enhancer elements are functional in vivo and drive expression in E12.5 transgenic mice. Sectioning planes indicated by red lines. Black line in (E) marks the expression in the dorsal neural tube, whereas rostral and caudal regions lack dorsal expression (black arrows). (H)- (J) Neural tube lacZ expression driven by (H) EE1: immature neuronal precursors (grey arrow), (I) EE2: dorsal neural tube (grey arrow) and dorsal root ganglia (black arrow), and (J) EE3: dorsal neural tube (grey arrow). Scale bars 100 µm.  K)- (M) Midbrain lacZ expression, driven by (K) EE1, (L) EE2 and (M) EE3. Black arrow indicates neuronal population from EE1 embryo stained in (N). Scale bars 100 µm. (N) EE1 drives expression in oculomotor complex; immunofluorescent co-staining with antibodies against ISL1/2 (motoneurons of oculomotor complex; red) and β-Gal (green). LacZ-staining of the region in (k); black arrow. Scale bars 50 µm.
Figure 4A: Cartoon representation of SARS-CoV-2 N-CTD. Ribbon representation of SARS-CoV-2 N-CTD showing the separated monomer and dimer. One monomer is coloured in pink, and the other is coloured in yellow. B: Rotation of (A) along the x-axis by 90° to show the top view. C: Topology diagram for SARS-CoV-2 N-CTD. The α-helices are numbered A, B and C, η represents the 310 helix and β represents the β-sheet, according to a previous SARS N-CTD structural element numbering rule (Yu et al, 2006).