EMBO/soda-nel huggingface dataset:
A common molecular logic determines embryonic stem cell self-renewal and reprogramming (2018)
Figure 7

Figure 7: A common gene regulatory program governs naïve state maintenance, EpiSC resetting and somatic cell reprogramming.

(A) 0.717 cABN predictions compared with published data on gene combinations that do (dark green) or do not (white) enable MEF reprogramming.

(B) Comparison of predictions (left) and experimental outcome (right) for the potency of additional network factors in OSKM-driven MEF reprogramming in LIF containing medium. n=4 independent experiments, except Klf2 and Nanog where n=2 independent experiments. * = p<0.05 Student's t-test. n.s. = not significant. Red dashed lines indicate empty vector + OSKM level. Box plots indicate min, median, max.

(C) Comparison of predictions (left) and experimental outcome (right) for the potency of additional network factors in OSKM-driven MEF reprogramming in 2i+LIF. n=4 independent experiments, except Klf2 and Nanog where n=2 independent experiments. * = p<0.05 Student's t-test. n.s. = not significant. Empty vector + OSKM reprogramming in LIF ("control no 2i") was included as a control for the effect of 2i addition. Red dashed lines indicate empty vector + OSKM control level. Box plots indicate min, median, max. The red asterisk indicates that the effect of Sall4 was incorrectly predicted.

(D) Recapitulation of the gene activation kinetics during MEF reprogramming. Top, the number of regulation steps required for permanent activation of the indicated gene. Tfcp2l1 and Sall4 are found to activate earlier than Nanog and Esrrb. Bottom, gene expression measured from sorted populations of reprogramming intermediates from O'Malley et al. (2013).

(E) Delineation of gene activation at single cell level. Top, experimental scheme used in Buganim et al. (2012) for the isolation of reprogramming intermediates profiled by single-cell RT-qPCR. Bottom, comparison of the predictions of the sequence of gene activation between gene pairs (left) along the reprogramming trajectory in OSKM+LIF, compared with experimental measurements from Buganim et al. (2012). Each table shows the percentage of single cells at the indicated stage of reprogramming (column) that have the indicated expression state of the gene pair considered (row).

(F) Summary of the predictive accuracy of the three cABNs progressively refined against experimental results, with the 0.717 cABN having the highest predictive accuracy for each set of the investigation.
SARS-CoV-2 and SARS-CoV Spike-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development (2020)
Figure 2.

Measurements of SARS-CoV-2 and SARS-CoV S1 binding to ACE2.A. Serial diluted recombinant S1 proteins of SARS-CoV-2, SARS-CoV and MERS-CoV were coated on 96 well plates, incubated with the recombinant Fc-tagged ACE2 (ACE2-Fc) for binding evaluation. B. Recombinant S1 proteins of SARS-CoV-2 and SARS-CoV were incubated with 293T-ACE2 cells and subjected to FACS evaluation for binding.
SARS-CoV-2 and SARS-CoV Spike-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development (2020)
Figure 3.

Cross-reactivity and neutralization efficiency of SARS nAbs against SARS-CoV-2.A. Binding of SARS nAbs to SARS-CoV S1 protein were tested by ELISA. Recombinant S1 protein of SARS-CoV were coated on plates, serial diluted nAbs were added for binding to recombinant S1 protein.B. Binding of SARS nAbs to SARS-CoV-2 S1 protein were tested by ELSIA. Recombinant S1 protein of SARS-CoV-2 were coated on plates, serial diluted nAbs were added for binding to recombinant S1 protein. C. Neutralization of SARS-CoV nAbs against SARS-CoV-2 PSV. D. Antibody competition with SARS-CoV RBD binding to ACE2. Recombinant SARS-CoV RBD protein was coated on plates, nAbs and recombinant ACE2 were then added for RBD binding competition measurements.
The BACE-1 inhibitor CNP520 for prevention trials in Alzheimer's disease (2018)
Figure 2

Figure 2. CNP520 treatment of male C57/BL6 mice for 8 weeks did not cause hair depigmentation. (A) Subjective assessment of hair depigmentation (score 0-5, with 0 = completely black and 5 = completely white) at 2 doses of either CNP520 or the BACE-1/-2 inhibitor NB-360 (Shimshek et al, 2016) (mean ± SEM, n=8/group), statistical comparisons were made for every scoring day, versus vehicle using Kruskal-Wallis with Dunn's post-hoc test. (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.
The BACE-1 inhibitor CNP520 for prevention trials in Alzheimer's disease (2018)
Figure 4

Figure 4. Chronic therapeutic treatment of APP23 mice with CNP520. Male APP23 mice (age at baseline: 12-14 months old) were dosed with CNP520 in food pellets for 6 months: Low dose 0.03 g CNP520/kg food, corresponding to a daily oral dose of 4 mg/kg; high dose 0.3 g/kg food, corresponding to a daily oral dose of 40 mg/kg. (A) CNP520 levels in blood and cerebellum. (B) Total cortical plaque area (normalized to total sample area (*10−2), stained with antibody NT-12. (C) Formic acid-soluble Aβ40 in forebrain. (D) Formic acid-soluble Aβ42 in forebrain. (E) Double-immunofluorescence stained brain sections with NT12 (against amyloid-β, green) and Iba1 (against microglia, red) or GFAP (astrocytes, red) for the different treatment groups as indicated. Scale bar: 500 µm. (F) Quantification of total Iba1 positive microglia (normalized to total area (*10−2), only a subset of samples analyzed. (G) Quantification of total GFAP positive astrocyte area (normalized to total area (*10−2). Data were analyzed with Dunnett's multiple comparison test.
The BACE-1 inhibitor CNP520 for prevention trials in Alzheimer's disease (2018)
Figure 6

Figure 6. Effects of CNP520 administration on major APP metabolites in the CSF of healthy study participants ≥ 60 years of age. (A) Changes in Aβ40 relative to baseline values. (B) Changes in sAPPβ relative to baseline values. (C) Changes in sAPPα relative to baseline values. (D) Dose response of Aβ40 (mean ± SD) to CNP520 relative to baseline Aβ40 levels after 2 weeks of dosing. (A-C) CSF was sampled via a lumbar catheter at time points from 2 hours pre- to 34 hours post-administration of a single dose of CNP520 (mean ± SEM, n = 6-8). (D) CNP520 was administered daily for 14 days; CSF was sampled via a lumbar catheter 2 hours before dosing, and 24 hours after the last dose (mean ± SD, n = 8 in treatment groups, n = 16 in placebo group).
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 2

Figure 2. Identification of zsp-1.

A) Complementation testing of gg661, gg662 and gg633 using dpy-11 RNAi inheritance defect. Hermaphrodites of indicated genotype were subjected to dpy-11 RNAi before being crossed with males of indicated genotype. F1 progeny, grown in the absence of dpy-11 RNAi, were scored for Dpy. Wild-type (WT).

B) Positional mapping of gg661, gg662 and gg633. Mutant animals were crossed with a mapping strain (see Materials and Methods). Progeny were subjected to dpy-11 RNAi and non-Dpy F2 progeny were pooled and genomic DNA isolated from pooled animals was subjected to whole genome sequencing. Y axis shows the percentage of sequence reads that harbored mapping strain single nucleotide polymorphisms (SNPs) as a function of the total number of reads that contained each SNP. The red line is a LOESS regression line through all the SNP points on Chr I. The data show that all three alleles are linked to the left arm of chromosome I.

C) zsp-1 alleles described in this study and predicted domains are indicated. aa, amino acid. IDR, intrinsically disordered domain. *, stop codon.

D) Animals harboring CRISPR-generated deletion alleles in y48g1c.1 (gg682 or gg683) were treated with dpy-11 RNAi and progeny, grown in the absence of dpy-11 RNAi, were scored for Dpy. Percentage of Dpy animals is shown. N=3, error bar is standard deviation, s.d.

E) Fluorescence micrograph of GFP::ZNFX-1 and PGL-1::TagRFP fluorescence in animals harboring a CRISPR-generated deletion allele (gg682) in y48g1c.1. Scale bar, 5μm.
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 3

Figure 3. ZSP-1 is a germline-expressed protein that segregates with the germline.

Fluorescence micrograph of gfp::zsp-1 at the indicated stages using a Nikon Eclipse Ti microscope equipped with a W1 Yokogawa Spinning disc under a 63X/1.4 Plan Apo oil objective. Scale bar, embryos: 5μm, germline: 10μm. Dashed lines indicate the outline of the adult germline.
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 4

Figure 4. ZSP-1 localizes to the outer periphery of Z granules.

A) Fluorescent micrographs of pachytene germ-cell nuclei from animals expressing indicated fluorescent proteins. Scale bar, 2μm.

B) 3D render of one set of GFP and TagRFP foci from panel A. Scale bar, 0.5μm.

C) Germlines dissected from animals expressing the indicated proteins were fixed and stained with α-FLAG and α-HA antibodies, followed by secondary antibodies conjugated with Alexa 488 and CF430, respectively. Pachytene germ-cell nuclei were imaged with a Leica TCS SP8 microscope. Scale bar, 2μm.

D) Quantification of the degree to which fluorescent signals from the indicated fluorescent proteins colocalize. See Fig. EV3A and Materials and Methods for details. For each group, 27 granules from 3 animals (3 cells per animal, 3 granules per cell) were quantified. Black line indicates mean of the degree of colocalization in each group.

E) Germlines dissected from animals expressing the indicated proteins were fixed and stained with α-GFP and α-HA or α-FLAG antibodies, followed by secondary antibodies conjugated with Alexa 488 and CF430, respectively. Pachytene germ-cell nuclei were imaged with a Leica TCS SP8 STED 3X microscope using 592nm to selectively deactivate fluorophores. Bottom panel. GFP::ZNFX-1 and HA::TagRFP::ZNFX-1 expressing animals were crossed and germlines of trans-heterozygous progeny from this cross were fixed and stained and imaged by STED as described above. Scale bar, 0.5μm.

F) Degree of colocalization of indicated fluorescent proteins in STED images was determined as described in Materials and Methods. For each group, 12 granules from 3 animals (4 granules per animal) were quantified. Black line indicates mean of the degree of colocalization in each group.
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 5

Figure 5. ZSP-1 regulates Z granule homeostasis.

A) Fluorescent micrographs of a pachytene stage germ- cell nuclei from WT or zsp-1(gg682) animals expressing the indicated fluorescent proteins. Scale bar, 2μm.

B-D) Z-stack confocal images from pachytene germ cells from animals of the indicated genotypes were analysed as described in Fig. EV4B and Materials and Methods to determine; the size of P or Z granules (panel B); the distribution of different sizes of P or Z granules in wild-type and zsp-1(gg682) animals (panel C); or the number of P or Z granules surrounding a typical nucleus in wild-type and zsp-1(gg682) animals (panel D). Granules from 9 total nuclei from 3 different animals (3 cells per animal) were quantified for these analyses. Black lines indicate mean of all data points in each group. P value, student's t test, two tailed.

E) Time-lapse imaging of the first embryonic cell division in zygotes of the indicated genotypes and expressing the indicated fluorescent proteins. Pronuclear meeting (pnm) time is defined as 0min. Times are relative to pnm. Scale bar, 5μm.

F) Fluorescent micrographs of four cell embryos of WT or zsp-1(gg682) expressing the indicated fluorescent proteins. Scale bar, 5μm.

G,H) GFP::ZNFX-1 (panel G) fluorescence or PGL-1::TagRFP fluorescence (panel H) in the anterior (A) or posterior (P) section of a one cell embryo. Anterior and posterior regions were determined based on corresponding DIC images. N=4 embryos for G, N=3 embryos for H. Error bars are +/- s.d.
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 6

Figure 6. ZSP-1 regulates Z granule fluidity and stability.

A) Heat map showing recovery of ZNFX-1 fluorescence after photobleaching in Z granules from pachytene stage adult germ cells from wild-type or zsp-1(gg682) mutant animals. Scale bar, 0.5 μm.

B) Normalized recovery of fluorescence after photobleaching of GFP::ZNFX-1 in wild-type or zsp-1(-) mutant animals over indicated time points. Bleaching event occurred at 0s. Data are represented as ± s.e.m. of n=13, and n=16 individual granules from wild-type and zsp-1(gg682) animals, respectively.
ZSP-1 is a Z Granule Surface Protein Required for Z Granule Fluidity and Germline Immortality in C. elegans (2020)
Figure 7

Figure 7. ZSP-1 promotes small RNA-based gene regulation and germline immortality.

A) Lineages of animals of the indicated genotypes were grown at 25°C or 20°C for the indicated generations. Each generation six animals were isolated in order to maintain the lineage and to determine numbers of progeny. Data are represented as +/- s.e.m. N=3 for generation 8 or 9, N=6 for all other generations.

B) Volcano plot showing log2 fold change of the number of endogenous siRNAs targeting each C. elegans gene in zsp-1(gg682) vs WT animals on x-axis and log10 (adjusted p-value) of changes on the y-axis. Dots in red indicate siRNAs pools targeting this gene were significantly different in zsp-1(gg682) and WT animals. Dashed lines indicate log2(fold change)=-1 or 1. Adjusted P-value was calculated using Benjamini Hochberg method in DEseq2.

C) Representation factor indicates the number of genes overlapping divided by the expected number of genes overlapping in two datasets, with a value of one (dashed line) indicating random overlap. A representation factor >1 indicates more overlap between datasets than expected by chance. Data show a comparison of lists of genes differentially targeted by endo siRNAs in zsp-1(gg682) animals relative to WT animals against lists of genes known to be targeted by CSR-1 (Claycomb et al. 2009), HRDE-1 (Buckley et al. 2012), WAGO-4 (Xu et al. 2018), or all WAGO-class endo siRNAs (Gu et al. 2009).

D) Venn diagram of the overlap between genes that are both regulated both ZSP-1 and targeted by WAGO-4 endo siRNAs and lists of genes targeted by either WAGO (Gu et al. 2009) or CSR-1-class endo siRNAs (Claycomb et al. 2009).

E) Fluorescent micrographs showing a piRNA sensor transgene (mex-5p::gfp::his-58::21UR-1::tbb-2 3'UTR) (Bagijn et al. 2012) expressing GFP in the -1 to -3 oocytes of adult C. elegans of the indicated genotypes. Scale bar, 20μm.

F) oma-1(zu405) is a temperature sensitive (ts) lethal (embryonic arrest at temperatures > 20°C) allele of oma-1 (R. Lin 2003). oma-1 RNAi suppresses oma-1(zu405ts) lethality. Animals were exposed to oma-1 RNAi and the number of embryos that hatched was scored at 20°C. N=3. Error bars are +/- s.d. Animals harboring mutations in genes specifically required for the inheritance of RNAi would respond normally to direct exposure to oma-1 dsRNA but fail to inherit this silencing (Wan et al. 2018). zsp-1 mutants fail to respond immediately to direct exposure to oma-1 dsRNA, indicating that ZSP-1 is not specific to inheritance and, therefore, is generally required for RNAi (see also Fig. EV5B-D).

G) RNAs of 16-30nts in length were sequenced from +/- oma-1 RNAi treated animals of the indicated genotypes. One replicate of the experiment is shown here and another replicate, which shows similar results, is shown in Fig. EV5E. Y axis shows # small RNA reads per million sequenced reads. X axis is the oma-1 gene.

Figure EV Legends
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 1

Figure 1. Mdm12 and Mmm1 Organization

A. Schematic diagrams showing the domain structures of Mdm12 and Mmm1 used in this study.

B. Size-exclusion chromatography (SEC) experiments of Mdm12, tMmm1, and the Mdm12-tMmm1 complex comparing the molecular size of these proteins in solution. The proteins indicated were injected into a Superdex 200 column (GE Healthcare) with a buffer containing 25 mM Tris-HCl (pH 7.5), 150 mM NaCl, and 5 mM DTT. The standard molecular masses for the SEC experiments (top) are shown for relative molecular weight comparison (blue dextran, void; ferritin, 440 kDa; aldolase, 158 kDa; cobalbumin, 75 kDa; ovalbumin, 44 kDa; and carbonic anhydrase, 29 kDa).

C. Graph indicating the molecular weights of Mdm12, His6-Mdm12, and the Mdm12-tMmm1 complex in solution as measured by analytical ultracentrifugation.
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 2

Figure 2. Overall Structure of Mdm12

A. Ribbon diagram of the yeast Mdm12 dimer. The crystal structure of full-length Mdm12 was determined by SAD and refined with native data to 3.1 Å resolution. Lipids bound to Mdm12 are drawn with black stick models.

B. Schematic diagram indicating the secondary structure elements and their organization in Mdm12. Three structural elements of Mdm12 are highlighted in different colored boxes.

C, D. Surface representations of the Mdm12 dimer are shown in different orientations.
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 3

Figure 3. Dimer Interface of Mdm12

A. Ribbon diagram showing the 2-fold dimerization interface of Mdm12. Oxygen and nitrogen atoms are shown in red and blue, respectively. The orange dotted lines indicate intermolecular hydrogen bonds between two protomers of Mdm12. The sequence alignment of yeast Mdm12 orthologs is shown to highlight the sequence conservation in the N-terminus β1-strand. Ten orthologs are aligned from residues 1 to 11. Absolute and highly conserved residues are indicated in red and orange, respectively.

B. The molecular weight of the Mdm12 (I5P) mutant was measured by size-exclusion chromatography (below) and ultracentrifugation (top) as in Figure 1B and C.

C. Ribbon diagram showing the structures of the SMP domain in E-SYT2, CETP, and BPI for the comparison of dimeric interfaces among SMP domains. Note that CETP and BPI are not dimers but monomers containing two tandem SMP domains.
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 4

Figure 4. Mdm12 Binds Lipid through the SMP Domain

A. Simulated annealing omit map (Fo-Fc, contoured at 1.5σ) showing the molecule bound to Mdm12 (left). The final model for the bound PE is shown as in stick representation. The electron density (2Fo-Fc) calculated in the final model is shown with the stick model of PE in the right (3.1 Å resolution, contoured at 0.8σ).

B. Surface representation of the Mdm12 dimer. Hydrophobic amino acids lining the Mdm12 channel are indicated by a blue mesh. Lipids built in Mdm12 are in space-filling representation.

C. Ribbon diagram showing lipid coordination by Mdm12. Mdm12 residues and lipid fatty acids are colored in green and yellow, respectively.

D. Mdm12 binds NBD-PE. Wild-type and monomeric (I5P mutant) Mdm12 were incubated with NBD-PE and separated from free NBD-PE in native PAGE. Coomassie staining (left) and fluorescent (right) detection indicates that Mdm12 directly interacts with NBD-PE in vitro.

E. Quantitative data showing binding affinities for NBD-PE by Mdm12. The binding affinities of Mdm12 (monomer/dimer shown in Native PAGE and I5P mutant) for NBD-PE was measured with a NBD-PE concentration-dependent manner. All experiments were carried out three times and the means ± SD are given.

F. Mdm12 mutants (L256W, I262W, and L256W/I262W double mutant) were incubated with NBD-PE, and subjected to native PAGE. Because wild-type Mdm12 separates as both monomer and dimer on native PAGE, the purely monomeric form (I5P) of Mdm12 was used as the wild type for clarity. The graph in the right indicates the quantities measured in the experiments. The bar shows the relative amounts of the band ratio (fluorescence/Coomassie). Values represent the means and SD from three independent experiments.
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 5

Figure 5. Glycerophospholipid Selectivity of Mdm12

A. Structural views suggesting that Mdm12 might have a preference for certain phospholipids. The surface representation of Mdm12 positioned around the binding site for the head group of PE is shown with charge distribution (left) and the sequence conservation (right) in the same orientation. Surface electrostatics and sequence conservation were calculated using an APBS program [31] with the nonlinear Poisson-Boltzmann equation and contoured at ±3kT/e, and ConSurf website (consurf.tau.ac.il) [32] with 34 different yeast orthologs, respectively. The ribbon diagram shown in the middle indicates the overall orientation of Mdm12.

B. Lipid displacement experiments to identity the natural ligands of Mdm12 in vitro (see material and methods section for details). NBD-PE-preloaded Mdm12-GST was mixed with a series of glycerophospholipids at different concentrations, and displacement of NBD-PE by non-labeled ligand was estimated from the decrease in fluorescence. Means ± SD are shown (n=3 independently performed experiments).
Crystal structure of Mdm12 reveals the architecture and dynamic organization of the ERMES complex (2016)
Figure 6

Figure 6. The Mdm12/ΔMdm12 Molecules in the Asymmetric Unit Provide an Insight into the Organization of the Mdm12-Mmm1 Binary Complex

A. Overall structure (left) and electron density (right) of Mdm12 in the asymmetric unit. Four molecules (two Mdm12 dimers) are organized with 2-fold rotation symmetry. The 2-fold axes are indicated with a black dotted line.

B. Overall structure (left) and electron density (right) of ΔMdm12 in the asymmetric unit. Six ΔMdm12 molecules (three Mdm12 dimers) are arranged with 2-fold rotation symmetry as shown above.

C. Ribbon diagram showing a 2-fold interface (tail-to-tail) in two crystal structures (See text for details).

D. Size-exclusion chromatography revealing that the N-terminus-truncated version of Mdm12 (residues 11–271) retains the ability to interact with Mmm1. The experiment was performed as in Figure 1B. Eluted fractions indicated by shading were subjected to SDS-PAGE followed by Coomassie Blue staining.
High grade mesenchymal pancreatic ductal adenocarcinoma drives stromal deactivation through CSF-1 (2020)
Figure 1

Fig 1. High-grade PDAC features stroma that is low in collagen and activated PSC content.

(A) Picrosirius red (PSR) staining of collagens (red) in PDAC tissue following surgical resection. Scale bar represents 200 µm.

(B) Quantification of PSR in low-grade (1-2) and high-grade (3) tumors indicated in panel A as percentage of area. n=15 primary PDAC samples.

(C) Quantification of tumor cell percentage as scored by pathologists in low- and high-grade PDAC indicated in panel A. n=15 primary PDAC samples.

(D) PSR and α-SMA staining of indicated PDAC cell lines which were injected in NSG mice. Scale bar represents 200 µm for PSR and 100 µm for α-SMA images.

(E) Quantification of stainings indicated in panel D. Three tumor ROIs of a tumor derived from epithelial cell lines (Capan-2 and AsPC-1) and mesenchymal cell lines (MIA PaCa-2 and PANC-1) are displayed and averages were pooled for analysis.

(F) IHC staining of α-SMA in 3D organotypic co-cultures of PS-1 cells and indicated PDAC cell lines. Scale bar represents 100 µm.

Data information: (B-E), data are represented as mean±SD, Student's t-test.