EMBO/soda-nel huggingface dataset:
Early auto-immune targeting of photoreceptor ribbon synapses in mouse models of multiple sclerosis (2018)
Figure 4

Figure 4. MOG/CFA- but not CFA-injected mice contain reactive antibodies for retinal proteins in blood and show altered spatial visual behavior. (A) 7-9 days after injection, blood from MOG/CFA-injected (red) but not from CFA-injected mice (black), elicited strong antibody responses in ELISA. Antibodies for RIBEYE and SV2 were used as positive controls (green), secondary antibody only as a negative control (white). Normalized data are given as mean ± S.E.M. (N=4 (CFA); N=5 (MOG/CFA). ** p<0.01 (significance was assessed by Mann-Whitney test, precise p-values given in the figure). (B) Control Western blot of HEK293 protein lysates obtained from cells transfected with mCherry (lane 1) or CASPR1-mCherry cDNA (lane 2) and probed with anti-mCherry antibody. (C,D) Western blot of protein lysates as in B) probed by blood samples from mice before and 7 to 9 days after MOG/CFA injection. Only blood samples obtained from MOG/CFA-injected mice revealed immunoreactivity against CASPR1 (lanes 15,16; top panels) whereas samples obtained before immunization (lanes 7,8; top panels) did not. The same filters were re-probed with anti-actin antibodies as loading control. (E) Summary of data from (C,D) shown as mean ± S.E.M. (N=4, before injection; N=5, MOG/CFA-injected). ***, p<0.001; n.s., non-significant (unpaired two-tailed Student's t-test, precise p-values given in the figure). (F) Spatially guided visual behavior, measured as frequency threshold with a virtual optokinetic system 9 days after immunization, is significantly decreased in MOG/CFA-injected mice compared to CFA-injected control litters. Data are shown as median; boxes and whiskers illustrate 25-75 and 5-95 percentiles of values, respectively. Points below and above whiskers are drawn as individual points. At each trial, mice were measured three times. Home-made and commercial MOG/CFA suspensions were compared as well as PLP-injected mice with control-injected mice. Statistical analysis was done by ANOVA (0,05 significance level), mean comparison probabilities were Bonferroni corrected. N=32, n=96 (MOG/CFA); N=24, n=72 (CFA). ***, p<0.001 (Mann-Whitney test). Results from mice injected with home-made and commercial MOG/CFA suspensions as well as results obtained from PLP/CFA-injected mice (and respective control-injected mice) are displayed.
Early auto-immune targeting of photoreceptor ribbon synapses in mouse models of multiple sclerosis (2018)
Figure 5

Figure 5. Optic nerve parameters are unaltered in early EAE (9 days after injection). (A,B) Cryostat sections of the optic nerve from MOG/CFA-injected mice (own lab-made suspension; for comparison with commercial MOG/CFA suspensions, see Appendix Fig. S12) and CFA-injected control mice were stained with anti-Nav antibody (1:50 dilution) to label the node of Ranvier and with anti-CASPR1 antibody (1:500 dilution) to stain the paranodal region. Length of the node of Ranvier and length of the paranodal region were quantified in C) D). (E1, E2) Richardson-Blue stained semi-thin sections from the indicated optic nerve samples. (E2, E3, F2, F3) Transmission electron micrographs of the optic nerves from MOG/CFA- and CFA-injected animals. Abbreviations: ax, axon; my, myelin sheath. Axon number and myelin thickness were quantified in G) and H). Scale bars: 1μm (A,B,E,F).
Early auto-immune targeting of photoreceptor ribbon synapses in mouse models of multiple sclerosis (2018)
Figure 6

Figure 6. Vesicle cycling in MOG/CFA-injected mice (injected with commercial MOG/CFA suspensions; Hooke kit) at day 9 after injection is strongly reduced in comparison to control mice. Retinal slices from MOG/CFA-injected and CFA-injected SypHy mice were stimulated by applying a 25mM K+-containing depolarization solution for 1min (Fig. 6A). In response to depolarization, we observed a strong increase in fluorescence (Fig. 6A) that can be best fitted by a double-exponential curve (B). Amplitudes of fast and slow release (together with the respective time constants) of the first depolarization response are plotted in C).
Early auto-immune targeting of photoreceptor ribbon synapses in mouse models of multiple sclerosis (2018)
Figure 7

Figure 7. The amount of CASPR1 protein in the synapse is also altered in the PLP mouse model of multiple sclerosis. Semi-thin sections of PLP/CFA and CFA-injected mice were probed with the indicated antibodies (A, B; see also Appendix Fig. S13). The synaptic amount of CASPR1 is strongly reduced both in the OPL and IPL. RIBEYE is only reduced in the OPL but not significantly in the IPL. CNTN1 is strongly reduced in both OPL and IPL (C, see also Appendix Fig. S13). N=4 PLP/CFA-injected mice; N=4 CFA-injected mice; n=140 slices (CFA, RIBEYE); n=143 slices (PLP/CFA, RIBEYE); n=47 slices (CFA, CASPR1); n=53 slices (PLP/CFA, CASPR1); n=49 slices (CFA, CNTN1); n=46 slices (PLP/CFA, CNTN1); n=44 slices (CFA, v-arrestin); n=44 slices (PLP/CFA, v-arrestin). (D,E) Cryostat sections of the optic nerve from PLP and control mice were stained with anti-Nav-channel antibody to label the node of Ranvier and with anti-CASPR1 antibody to stain the paranodal region. Length of the node of Ranvier and length of the paranodal region were quantified in G) H). (F) transmission electron micrographs of the optic nerves from PLP/CFA- and CFA-injected animals (F1-F4). Axon numbers and myelin thickness were quantified in I) J).
NOD2 enhances the innate response of alveolar macrophages to Mycobacterium tuberculosis in humans (2011)
Figure 1

NOD2 accounts for intracellular pathogen sensing receptors in human alveolar macrophages. (A) Intracellular detection of NOD2 (bold line in the histogram plot) was performed by flow cytometry using freshly isolated alveolar macrophages selected from a gate set on large granular bronchoalveolar cells (R1, dot plot). One representative experiment out of three experiments is presented. (B) Cells were stimulated with 10 μg/mL of MDP for 24 h, and NOD2 and IκBα proteins were measured in the cytosolic fractions by western blot analysis. The fold increase relative to unstimulated cells and normalized to tubulin of one representative experiment out of three is reported. (C) The upregulation of NOD2 gene expression was assessed by quantitative PCR. The results are depicted as the mean fold change in NOD2 gene expression relative to unstimulated cells (n = 11). (D) Subcellular localization of NOD2 was ascertained in unstimulated (left, ×80,000) and MDP‐stimulated cells (right, ×63,000) using an anti‐NOD2 antibody and detected with a secondary antibody coupled to 5‐nm gold particles, indicated with arrowheads. Bar represents 150 nm. Micrographs were obtained from one experiment.
NOD2 enhances the innate response of alveolar macrophages to Mycobacterium tuberculosis in humans (2011)
Figure 2

NOD2 ligation in alveolar macrophages induces pro‐inflammatory cytokine release. Cells were incubated for 24 h in the presence of 10 μg/mL of MDP or 100 ng/mL of LPS. Production of IL‐1β, IL‐6, TNF‐α, and IL‐10 was measured in culture supernatants using Milliplex technology. Depicted are box plots with median values and quartiles for each cytokine. The data are representative of two independent experiments (n = 11); *p 0.05 and **p 0.01 using the two‐tailed Wilcoxon signed‐rank test.
NOD2 enhances the innate response of alveolar macrophages to Mycobacterium tuberculosis in humans (2011)
Figure 3

LL37 and IRGM gene expression is upregulated following NOD2 activation (A‐D). Alveolar macrophages were incubated in the presence of 10 μg/mL of MDP or 100 ng/mL of LPS for 24 h. Upregulation of (A) LL37 and (D) IRGM gene expression was assessed after specific ligand recognition by quantitative PCR using the Taqman system and the ΔΔCT method for relative quantification. The fold change in gene expression relative to unstimulated cells is depicted. Data are representative of two independent experiments (n = 7–12). Bold lines indicate median values. (B, E) LL37 and IRGM protein levels were measured in cytosolic fractions by western blot analysis. (C, F) Data are expressed as the protein fold increases relative to unstimulated cells and normalized to tubulin calculated by densitometry and are shown as means ± SEM. One representative experiment out of three experiments is presented.
NOD2 enhances the innate response of alveolar macrophages to Mycobacterium tuberculosis in humans (2011)
Figure 4

NOD2 activation after M. tuberculosis infection induces an antibacterial innate activation profile. Alveolar macrophages were infected with M. tuberculosis H37Rv at an infection ratio of 1–2 bacteria/20 macrophages for 1 h. Nonphagocytosed bacteria were washed away, and the macrophages were then treated with 10 μg/mL of MDP or left with medium alone. (A) Intracellular bacterial burden was measured by quantifying CFU, and the intracellular growth index was calculated after 1 and 4 days post infection relative to phagocytosed bacteria at day 0. Data are shown as medians and quartiles and are representative of n = 7 experiments. The production of (B) TNF‐α, (C) IL‐6 and (D) IL‐1β was measured in culture supernatants using Milliplex technology. Box plots depicting median values and quartiles are representative of n = 9 experiments. (E) LL37 and (F) IRGM gene expression was assessed by quantitative PCR using the Taqman system and the ΔΔCT method for relative quantification. Fold changes in gene expression relative to unstimulated cells are reported. Bold lines indicate median values of n = 9. *p 0.05 and **p 0.01 using the two‐tailed Wilcoxon signed‐rank test. (G) LL37 and IRGM protein was assessed by western blot. One representative experiment out of three experiments is presented. (H) The amount of protein normalized to tubulin relative to infected‐only cells was calculated by densitometry. Data are depicted as the means ± SEM and are representative of n = 3 experiments.
NOD2 enhances the innate response of alveolar macrophages to Mycobacterium tuberculosis in humans (2011)
Figure 5

NOD2 activation of M. tuberculosis‐infected macrophages induces the recruitment of autophagy proteins IRGM, LC3, and ATG16L1 to the bacteria‐containing vesicles. Alveolar macrophages were infected with M. tuberculosis H37Rv at an MOI of 5 for 1 h. Nonphagocytosed bacteria were washed away, and the macrophages were incubated for an additional hour. The cells were then treated with 10 μg/mL of MDP for 24 h or left with medium alone. (A, B, D, E, G, H) The subcellular localization of autophagy proteins was ascertained in untreated and MDP‐treated cells using (A, B) anti‐IRGM, (D, E) anti‐LC3, and (G, H) anti‐ATG16L1 antibodies and detected with a secondary antibody coupled to 5‐nm gold particles indicated with arrowheads; bar represents 150 nm. (C, F, I) Gold particles co‐localizing with bacteria were manually counted in ten macrophages of each condition. Means ± SEM are depicted and differences between treatments are indicated, *p 0.05 using a two‐tailed paired t‐test. (B) Transmission electron microscopy (TEM) magnification ×50,000; the rest of the micrographs are TEM magnification ×80,000. Data were generated from one experiment.
Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens (2021)
Figure 1

Figure 1 - VpT6SS1 is functional in V. natriegens.

A Schematic representation of the V. parahaemolyticus RIMD 2210633 T6SS1 gene cluster. Genes are represented by arrows indicating the direction of transcription. Locus numbers (vpxxxx) are denoted above. Notable T6SS components are denoted below.

B Expression (cells) and secretion (media) of VgrG1 from V. parahaemolyticus RIMD 2210633 derivative POR1 (Vpara; T6SS1+) and its T6SS1- mutant (Vpara/∆hcp1), and from V. natriegens (Vnat) carrying the indicated plasmids. Samples were treated (+) or not (-) with 20 µM phenamil to activate surface sensing in media containing 3% NaCl at 30 °C for 5 h. Loading control (LC) is shown for total protein lysates. Arrows denote bands corresponding to VgrG1. Asterisks denote non-specific bands detected in Vnat samples.

C Viability counts of V. natriegens prey before (0 h) and after (4 h) co-incubation with the indicated attackers, as described in B, on media containing 3% NaCl at 30 °C. Data are shown as the mean ± SD, n = 3 technical replicates. Statistical significance between samples at the 4 h timepoint by an unpaired, two-tailed Student's t-test is denoted above. A significant difference was considered as P < 0.05. DL, assay detection limit.

D Illustration of interbacterial competition mediated by VpT6SS1 when introduced into V. natriegens (yellow) on a plasmid (pT6SS1), as shown in C. Prey cells are denoted in blue.
Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens (2021)
Figure 2

Figure 2 - VP1407 can serve as an effective on/off switch for VpT6SS1 in V. natriegens.

A Illustration of the VpT6SS1 (vp1386-vp1420) activation cascade. Genes are represented by arrows indicating the direction of transcription. Genes belonging to the same operon are denoted by the same color. Locus numbers (vpxxxx) are denoted above. Positive regulators are denoted by a red frame. Dashed arrows denote transcriptional activation and are color coded according to the relevant induced operon. Numbers in black circles next to the positive regulators TfoY, VP1407, and VP1391 delineate the progression of the cascade.

B Viability counts of V. natriegens prey before (0 h) and after (4 h) co-incubation with wild type V. natriegens attackers harboring the indicated plasmids, on media containing 3% NaCl at 30 °C.

C Expression (cells) and secretion (media) of VgrG1 from V. natriegens containing an arabinose-inducible vp1407 in the chromosomal dns locus (VnatReg) and harboring an empty plasmid (pEmpty) or plasmids containing VpT6SS1 that lacks vp1407 (pT6SS1Ind) or both vp1407 and hcp1 (pT6SS1Ind/∆hcp1; T6SS-). Samples were grown in media containing 3% NaCl and either supplemented (+) or not (-) with 0.1% arabinose (Ara) at 30 °C. Loading control (LC) is shown for total protein lysates.

D Illustration of the engineered VnatReg (yellow bacteria) containing a plasmid-borne, inducible VpT6SS1 (pT6SS1Ind). In the presence of arabinose (red circles), VP1407 is expressed from the chromosome and the plasmid-borne T6SS is induced, resulting in T6SS-mediated intoxication of adjacent prey bacteria (blue).

E Viability counts of V. natriegens prey before (0 h) and after (4 h) co-incubation with VnatReg attackers carrying the indicated plasmids on solid media plates, as described in C.

Data information: For B and E, data are shown as the mean ± SD, n = 3 technical replicates; statistical significance between samples at the 4 h timepoint by an unpaired, two-tailed Student's t-test is denoted above and is color coded to match the relevant samples. A significant difference was considered as P < 0.05.
Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens (2021)
Figure 4

Figure 4 - Manipulating the effector repertoire and target range of the VpT6SS1-based platform.

Viability counts of V. natriegens (cyan), V. vulnificus (purple), A. jandaei ∆tssB (brown), E. coli (green), and S. enterica (gray) prey before (0 h) and after (4 h) co-incubation with VnatReg attackers (yellow) harboring the indicated plasmids, on media containing 3% NaCl at 28 °C. The left panels show prey survival when competing alone (single prey) against the attacker at a 4:1 (attacker:prey) ratio; the right panels show the results of a competition experiment in which all prey were mixed together with the attacker at a 10:1:1:1:1:1 (attacker:prey) ratio. Data are shown as the mean ± SD, n = 3 technical replicates. Statistical significance between samples at the 4 h timepoint by an unpaired, two-tailed Student's t-test is denoted above and is color coded to match the relevant samples. A significant difference was considered as P < 0.05.
Engineering a customizable antibacterial T6SS-based platform in Vibrio natriegens (2021)
Figure 5

Figure 5 - Effector and immunity combinations alter the VpT6SS1-based platform's toxicity range.

A-D (A, B, D) Viability counts of V. parahaemolyticus RIMD 2210633 ∆hcp1 (A), V. alginolyticus 12G01 ∆hcp1/∆hcp2 (B), and V. natriegens (D) prey bacteria before (0 h) and after (4 h) co-incubation with VnatReg attackers harboring the indicated plasmids, on media containing 3% NaCl and 0.1% arabinose at 28 °C. Data are shown as the mean ± SD, n = 3 technical replicates. Statistical significance between samples at the 4 h timepoint by an unpaired, two-tailed Student's t-test is denoted above. A significant difference was considered as P < 0.05. ( C) Illustration summarizing the competitions shown in (A, B). Effector and immunity modules expressed by VnatReg carrying pT6SSEffectorless (yellow) are colored to match the bacterium from which they were derived.

Expanded Figure Legends
Gastric stem cells promote inflammation and gland remodeling in response to H. pylori via Rsp3-Lgr4 axis (2022)
Figure 1

Figure 1 - Lgr5 is dispensable for gastric gland hyperplasia, gland base expansion and antimicrobial defense upon infection with Helicobacter pylori.

Lgr5fl/fl/Axin2CreErt2 (Lgr5-/-) and control mice were infected for 2 months with H. pylori.

A Representative H&E staining from antral glands (upper row). The dotted line marks the gland base cell area, which expands upon infection in Lgr5-/- and control mice. Immunofluorescence labeling for GSII and Ki67 (middle row) and GIF and Muc5ac (lower row) of antral epithelium from Lgr5-/- and control mice uninfected and after 2 months of infection. Scale bars: 50 µm.

B Quantification of antral gland height in Lgr5-/- compared to control mice. Uninfected control (n = 5) versus uninfected Lgr5-/- (n = 4) versus infected control (n = 4) versus infected Lgr5-/- (n = 4).

C Quantifications of GSII+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse), Ki67 as percentage of total DAPI-stained cells (n = 3-4 biological replicates per group, n = 20 glands per mouse), GIF+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse), Muc5ac+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse).

D H. pylori CFUs in Lgr5-/- (n = 5) and control mice (n = 5).

E qPCR expression levels of Lgr4, Lgr5, Axin2, gland base cell markers (Gif, Pgc, Tff2, Muc6), pit cell marker Muc5ac, and Itln1 in uninfected Lgr5-/- (n = 6-10) and control mice (n = 4-10).

F qPCR expression levels of Lgr4, Lgr5, gland base cell markers (Gif, Pgc, Muc6), and Itln1 in Lgr5-/- (n = 5) and control mice (n = 5) after 2 months of infection.

Data information: For B, C, D, E and F, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for B, C, t-test for D, E and F).
Gastric stem cells promote inflammation and gland remodeling in response to H. pylori via Rsp3-Lgr4 axis (2022)
Figure 2

Figure 2 - Lgr4 regulates hyperplasia and expansion of gland base cells upon infection with Helicobacter pylori.

Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) and control mice were infected for 2 months with H. pylori.

A Representative H&E staining from antral glands (upper row). The dotted line marks the gland base cell area, which does not expand in infected Lgr4-/- but does expand in the corresponding control mice. Immunofluorescence labeling for GSII and Ki67 (middle row) and GIF and Muc5ac (bottom row) of antral epithelium from Lgr4-/- and control mice uninfected and after 2 months of infection. Scale bars: 50 µm.

B Quantification of antral gland height in Lgr4-/- compared to control mice. Uninfected control (n = 2) versus uninfected Lgr4-/- (n = 4) versus infected control (n = 4) versus infected Lgr4-/- (n = 4).

C Quantifications of GSII+ area (n = 2-4 biological replicates per group, n = 10 glands per mouse), Ki67 as percentage of total DAPI-stained cells (n = 2-4 biological replicates per group, n = 20 glands per mouse), GIF+ area (n = 2-4 biological replicates per group, n = 10 glands per mouse), Muc5ac+ area (n = 4-5 biological replicates per group, n = 10 glands per mouse).

D H. pylori CFUs show higher colonization in Lgr4-/- (n = 5) compared to control mice (n = 4).

E qPCR expression levels of Lgr4, Lgr5, Axin2, gland base cell markers (Gif, Pgc, Tff2, Muc6), pit cell marker Muc5ac, and Itln1 in uninfected Lgr4-/- (n = 4-10) and control mice (n = 4-6).

F qPCR expression levels of Lgr4, Lgr5, gland base cell markers (Gif, Pgc, Muc6), and Itln1 in Lgr4-/- (n = 5) and control mice (n = 5) after 2 months of infection.

Data information: For B, C, D, E and F, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001; **** = p < 0.0001; ns = not significant (one-way ANOVA + Tukey´s multiple comparison test for B, C, t-test for D, E and F).
Gastric stem cells promote inflammation and gland remodeling in response to H. pylori via Rsp3-Lgr4 axis (2022)
Figure 3

Figure 3 - Lgr4 regulates stem cells and NF-κB signaling in the antrum.

A, B GSEA comparing microarray data from 2-month infected Lgr4fl/fl/Axin2CreErt2 (Lgr4-/-) mice with publicly available data demonstrating downregulation of antral stem cell signature (A) and beta-catenin targets (B).

C qPCR expression levels for beta catenin targets Axin2 and Sox9 in uninfected and infected Lgr4-/- and control mice (n = 2-9).

D GSEA comparing microarray data from 2-month infected Lgr4-/- mice with publicly available data demonstrating downregulation of the TNF-α signaling via NF-κB.

E Immunofluorescence labeling for p65, Ki67 and GSII in the mouse antrum tissue from uninfected and infected Lgr4-/- and control mice. Insets show magnified images. Scale bars: 50 µm.

F Quantification of p65+ area as percentage of total DAPI-stained cells of uninfected and infected Lgr4-/- and control mice (n = 4 biological replicates per group, n = 20 glands per mouse).

G Immunofluorescence co-localization of p65 acetyl K310 (activated form of NF-κB) in the mouse antrum tissue of infected Lgr4-/- and in control mice. Insets show magnified images. Scale bars: 50µm.

H qPCR expression levels of Cxcl1, Cxcl2, Cxcl10, Ccl2 in uninfected and infected Lgr4-/- mice (n = 4-5) and control mice (n = 2-5).

I Immunofluorescence labeling for Cxcl1 in the mouse antrum tissue in infected Lgr4-/- and in control mice. Scale bars: 50 µm.

Data information: For G and I images represent findings that were reproduced at least twice in the laboratory in independent biological replicates. For C, F and H, data are mean + SD. * = p < 0.05; ** = p < 0.01; *** = p < 0.001 (one-way ANOVA + Tukey´s multiple comparison test).