Journal: AIMS Microbiology

Article Title: Fungal photoinactivation doses for UV radiation and visible light–a data collection

doi: 10.3934/microbiol.2024032

Figure Lengend Snippet: Log-reduction doses in mJ/cm 2 for Far-UVC, UVC and UVB for different fungi and various sample media. Besides the exact wavelength, additional information on strain, medium, temperature, and pH is given, if available.

Article Snippet: Aspergillus flavus , s , , median liquid: 163.3 5.2 (254 nm, JCM 2061, water, ); 35.6 (254 nm, liquid, 20 °C, pH 7.9, ); 291 (254 nm, KCCM 60330, liquid, ); 331 (254 nm, FRR 5660, liquid, ); 6.1 (280 nm, ATCC 46110, air, ); 35 (254 nm, ATCC 9296, agar, ); 85.3 (254 nm, FRR 5660, agar, ); 3429 (254 nm, KCCM 60330, round coffee beans, ); , .

Techniques: Saline

Journal: bioRxiv

Article Title: Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo

doi: 10.1101/2024.07.12.603270

Figure Lengend Snippet: (a) Wildtype zebrafish embryos were injected at the one-cell stage with 100 ng/μL of PAX3::FOXO1 (P3F) or equal molarity of control (CNTL) mRNA. (b) Schematic of embryonic zebrafish development with positioning of primary germ layers at key time points used in experiments. (c) Representative merged, phase contrast, and GFP images of zebrafish embryos at 3, 6, and 9 developmental hours-post-fertilization (hpf). Scale bar, 1 mm. (d) Representative western blot with protein lysate from 12 embryos per lane for each condition and 8 μg of protein lysate from RH30 cells, a PAX3::FOXO1-positive patient-derived cell line. The PAX3::FOXO1 time-course was repeated for a total of four replicates. Normalized quantification for the representative western blot of PAX3::FOXO1/αTUBULIN signal compared to RH30 cells is on the right, n=1.

Article Snippet: For spike-in normalization, PAX3::FOXO1-positive RH30 patient-derived cells RH30 (ATCC, CRL-2061) were fixed and stored like the zebrafish samples following their expansion and lifting with TrypLE Express (ThermoFisher Scientific, 12604013).

Techniques: Injection, Control, Western Blot, Derivative Assay

Journal: bioRxiv

Article Title: Rhabdomyosarcoma fusion oncoprotein initially pioneers a neural signature in vivo

doi: 10.1101/2024.07.12.603270

Figure Lengend Snippet: (a) Quantification of raw integrated density of GFP fluorescence. Each point represents an individual embryo, which were collected across three different injection days. Control-injected (CNTL) embryos: n=29 per time point, PAX3::FOXO1-injected (P3F) embryos: n=30 at 3 and 9 developmental hours post-fertilization (hpf), n=29 at 6 hpf. A Brown-Forythe and Welch ANOVA test with a Benjamini, Krieger, and Yekutieli correction for multiple comparisons was used to determine statistical significance. Asterisks represents statistics between P3F embryos. CNTL embryos across time-points had p≤0.005. Error bars indicate standard deviation. (b) Flow cytometry for GFP of 24 hpf wildtype (WT) uninjected zebrafish embryo as negative control. (c, d) Flow cytometry for GFP of zebrafish embryos injected with 50 ng/μL of PAX3::FOXO1 and 50 ng/uL pCS2-tagRFPT.zf1 at 6 and 12 hpf, respectively. (e) Protein sequence BLAST alignment between human FOXO1 and zebrafish orthologs Foxo1a and Foxo1b. (f) Western blot with protein lysate from 15 embryos per lane for each condition and 10 μg of protein lysate from RH30 cells, a PAX3::FOXO1-positive patient-derived cell line. Endogenous FOXO1 is detected in the patient-derived sample but not in zebrafish embryos. WT – Wildtype. *** denotes p<0.001 and ** denotes 0.001

Article Snippet: For spike-in normalization, PAX3::FOXO1-positive RH30 patient-derived cells RH30 (ATCC, CRL-2061) were fixed and stored like the zebrafish samples following their expansion and lifting with TrypLE Express (ThermoFisher Scientific, 12604013).

Techniques: Fluorescence, Injection, Control, Standard Deviation, Flow Cytometry, Negative Control, Sequencing, Western Blot, Derivative Assay

Journal: Nature Communications

Article Title: Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression

doi: 10.1038/s41467-024-47649-y

Figure Lengend Snippet: A – C Representative histogram of cell surface expression of 3 out of 5 PDX samples for VCAN (variable (var) exon), FN1 (EDB), and COL11A1. Tumor cell lines (A673, A549, LM7) served as positive controls (pos Co) and normal fibroblasts (Fib 1) or A549 FN-/- as negative controls (neg Co). D Heat map displaying cell surface expression in PDX samples as determined by flow cytometry ( n = 5 per tumor type). OS osteosarcoma, EWS Ewing’s sarcoma, RMS rhabdomyosarcoma, Co control, Fib normal fibroblast ( n = 1 per target, average of 3 technical replicates, negative and positive controls same as panel 3 A – C ). E RTqPCR for EDB or COL11A1 gene expression performed on PDX samples. Delta CT calculated relative to GAPDH. Dashed line: threshold of positivity based on qPCR results of antigen negative cells. F CAR expression determined by flow cytometry using an anti-mouse IgG F(ab’)2 ( n = 7 biologically independent samples, two-way ANOVA, **** p < 0.0001). G COL11A1 expression of LM7, 143B, CCL-136, CRL-2061, and A673 tumor cells, and two primary fibroblast cell lines (Fib 1, Fib 2) determined by RT-qPCR. Triplicates for each cell line are shown; COL11A1 expression in fibroblast was undetectable and their ΔCT value was set as 20. H NT or COL11A1-CAR T-cells were incubated at a 2:1 E:T ratio for 48 h with tumor cells or primary fibroblasts. Media only samples served as controls. IFNγ in culture media was determined by ELISA ( n = 3) for Fib 1, 4, and 7, n = 4 for all other conditions, biologically independent donors, two-way ANOVA of log-transformed data comparing against the NT of each tumor type to COL11A1 of each tumor type; **** p < 0.0001. All fibroblast experiments were non-significant. I Cytolytic activity of NT or COL11A1-CAR T-cells at an E:T ratio of 4:1 for 72 h against GFP.ffluc-expressing tumor cells or primary fibroblasts ( n = 3 for 143B, CCL-136, CRL-2061 (COL11A1-CAR and NT), and Fib 1, 4, 7, n = 4 for all other conditions, biologically independent donors, two-way ANOVA, comparing against the NT of each tumor type to COL11A1 of each tumor type ** p = 0.0058, **** p < 0.0001). All fibroblast experiments were non-significant.

Article Snippet: 143B (OS, CRL-8303), CRL-2061 and CCL-136 (RMS), and A673 (EWS, CRL-1598) cell lines were purchased from the American Type Tissue Collection (ATCC).

Techniques: Expressing, Flow Cytometry, Quantitative RT-PCR, Incubation, Enzyme-linked Immunosorbent Assay, Transformation Assay, Activity Assay