type strain  (ATCC)

Journal: iScience

Article Title: MAP3K1 integrates RhoA/ROCK signaling to regulate epithelial morphogenesis

doi: 10.1016/j.isci.2026.115853

Figure Lengend Snippet: S1P activates the MAP3K1-RhoA signaling network (A) Western blot and (B) densitometric analysis of phosphoproteins in wild type and Map3k1 −/− keratinocytes treated with S1P (10 μM, 1h). (C) Western blot and (D) quantification of phosphoproteins (p) in Map3k1 TG keratinocytes infected with Ad-GFP or Ad-Cre, with or without MAP2K4/7 inhibitor (BSJ-04-122, BSJ) or JNK inhibitor (SP600125, SP). (E) Quantification of p -PXN (Y) in S1P-treated HEK293 cells (Control, Ctl), cells expressing kinase dead MAP3K1 (KM), or cells with siRNA-mediated MAP3K1 knockdown (siRNA), and in Ad-Cre infected Map3k1TG keratinocytes treated with MAP2K4/7, JNK, or ROCK (Y27632, Y) inhibitors. (F) p -PXN (Y) in S1P-treated wild-type cells with or without ROCK inhibitor (Y) and in Rhoa Δ/Δ ;Rock1 Δ/Δ cells ( R Δ/Δ ;R Δ/Δ ) keratinocytes. (G) Quantification of CN03 (RhoA activator)-induced phosphoproteins in HEK293 cells expressing MAP3K1-KM. (H) S1P-stimulated AP-1 reporter activity and (I) Wound-closure assays in keratinocytes under the indicated genetic perturbations and inhibitor treatments. (J) Schematic model of MAP3K1 signaling network. Data represent mean ± SEM. from ≥3 independent biological replicates. ∗∗∗ p < 0.001 in (B and G) (unpaired two-tailed t test); ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001 in (D-F and H-I) (one-way ANOVA followed by Dunnett’s post hoc test).

Article Snippet: Wild type C57BL/6J strain , The Jackson Laboratory , RRID:IMSR_JAX:000664.

Techniques: Western Blot, Infection, Control, Expressing, Knockdown, Activity Assay, Two Tailed Test

Journal: iScience

Article Title: MAP3K1 integrates RhoA/ROCK signaling to regulate epithelial morphogenesis

doi: 10.1016/j.isci.2026.115853

Figure Lengend Snippet: G protein subunits and RhoGEFs connect S1P signaling to RhoA and MAP3K1 activation (A) Schematic model depicting candidate molecular links between S1P receptors, MAP3K1, and RhoA. (B and D) Western blot analyses and (C and E) quantification of phosphoproteins in S1P-treated HEK293 cells in the presence or absence of Gβ inhibitor (Gallein) or siRNAs targeting ARHGEF1 and ARHGEF5 (SC, scrambled control). (F) AP-1 reporter activity in S1P-treated HEK293 cells or MAP3K1-wild type (MAP3K1-WT) adenovirus infected cells with or without pathway inhibitors or ARHGEF knockdown. Data represent mean ± SEM. from ≥3 independent experiments. ∗∗∗ p < 0.001 in (C) (unpaired two-tailed t test); ∗∗ p < 0.01 and ∗∗∗ p < 0.001 in (E and F) (one-way ANOVA followed by Dunnett’s post hoc test).

Article Snippet: Wild type C57BL/6J strain , The Jackson Laboratory , RRID:IMSR_JAX:000664.

Techniques: Activation Assay, Western Blot, Control, Activity Assay, Infection, Knockdown, Two Tailed Test

Journal: iScience

Article Title: MAP3K1 integrates RhoA/ROCK signaling to regulate epithelial morphogenesis

doi: 10.1016/j.isci.2026.115853

Figure Lengend Snippet: G×G and G×E interactions converge on cytoskeleton reorganization (A) Gross eye images at birth (P0) and H&E-stained sections of wild type and Rhoa Δ/Δ ;Rock1 Δ/Δ embryonic eyes at E14.5-E16.5. Red arrows indicate open eye at birth (EOB) defects and the eyelid leading edge. (B) Phalloidin staining and (C) quantification of actin filaments (green) in wild type and Rhoa Δ/Δ ;Rock1 Δ/Δ ( R Δ/Δ ;R Δ/Δ ) eyelid epithelium at E15.5. Left: low magnification; right: enlargements of boxed areas. White arrowheads in (B) mark enriched F-actin at the epithelial leading edge. Dashed lines denote the basement membrane. (D) Phalloidin staining (red) and (E) quantification of F-actin in Rhoa flox/flox ;Rock1 flox/flox keratinocytes infected with Ad-GFP or Ad-GFP-Cre; only GFP positive cells were analyzed. Nuclei are counterstained with Hoechst (blue). Quantification of F-actin intensity in (F) TCDD-treated wild type and Rock1 Δ/Δ pups and (G) Ad-GFP (wild type) and Ad-GFP-Cre infected Rock1 flox/flox ( Rock1 Δ/Δ ) keratinocytes with or without TCDD treatment. Images are representative of at least three mice/genotypes or experimental replicates. CO, cornea; LE, lens; EL, eyelid; RE, retina. Data represent mean ± SEM. ∗∗ p < 0.01 and ∗∗∗ p < 0.001 in (C, E-F) (unpaired two-tailed t test), ∗∗ p < 0.01 in (G) (one-way ANOVA followed by Dunnett’s post hoc test). Scale bars, 500 μm and 200 μm (A) and 50 μm (B and D).

Article Snippet: Wild type C57BL/6J strain , The Jackson Laboratory , RRID:IMSR_JAX:000664.

Techniques: Staining, Membrane, Infection, Two Tailed Test

Journal: iScience

Article Title: MAP3K1 integrates RhoA/ROCK signaling to regulate epithelial morphogenesis

doi: 10.1016/j.isci.2026.115853

Figure Lengend Snippet: Genetic and environmental interactions regulate epithelial differentiation (A) Cell proliferation in wild type and Rhoa Δ/Δ ;Rock1 Δ/Δ ( R Δ/Δ ;R Δ/Δ ) eyelid at E15.5 assessed by EdU labeling. (B) Immunostaining and (C) quantification of Krt1 (green) as a marker of terminal epidermal differentiation in E15.5 eyelids of the indicated genotypes with or without TCDD exposure. Left: low magnification, right: enlarged boxed areas. Dashed lines mark the basement membrane. Nuclei are counterstained with Hoechst (blue). Images represent at least three embryos/genotypes or independent experiments. EL, eyelid. (D and E) RT-qPCR quantification of Krt1 (D) and Krt10 (E) mRNA in Ad-GFP-infected (wild type), Ad-Cre-infected Rock1 flox/flox ( Rock1 Δ/Δ ) and Rhoa flox/flox ; Rock1 flox/flox ( Rhoa Δ/Δ ; Rock1 Δ/Δ ) keratinocytes with or without TCDD treatment. Data represent mean ± SEM. ∗∗ p < 0.01 in (A) (unpaired two-tailed t test) and ∗ p < 0.05, ∗∗ p < 0.01, and ∗∗∗ p < 0.001 in (C-E) (one-way ANOVA followed by Dunnett’s post hoc test). Scale bars, 50 μm.

Article Snippet: Wild type C57BL/6J strain , The Jackson Laboratory , RRID:IMSR_JAX:000664.

Techniques: Labeling, Immunostaining, Marker, Membrane, Quantitative RT-PCR, Infection, Two Tailed Test

Journal: Computational and Structural Biotechnology Journal

Article Title: Next-Generation Sequencing Dataset Downloader and In Silico Sequence Mining: Graphical-User-Interface-Based Tools for Accessible, Multiprobe Target Mining in Next-Generation Sequencing Data

doi: 10.34133/csbj.0095

Figure Lengend Snippet: ISSM analysis of an NGS dataset obtained from CRFK cells infected with feline coronavirus (FCoV), using probes targeting various coronavirus groups, other viruses, CRFK cell sequences, and beta-actin. (A) Heatmap output generated by the ISSM. Probe sequences are color coded according to their target: SARS-CoV-2 (red), SARS-CoV (brown), Bovine CoV (yellow), Alphacoronavirus (blue), Universal coronavirus (green), Bat-CoV (purple), Feline coronavirus (gray), other viruses (black), CRFK cell (light orange), and beta-actin (pink). Color intensity indicates the relative number of matched reads, with deeper red representing higher read counts. (B) Relationship between extraction fraction and detected matched read proportion. Matched read counts obtained at 1%, 10%, 25%, and 50% extraction were expressed as percentages relative to the corresponding matched read counts obtained under 100% extraction, and a linear regression trendline was fitted to model this relationship. (C) Back-calculated 100% equivalent matched read counts derived from the regression equation shown in panel (B), compared with the actual matched read counts obtained under 100% extraction. The actual 100% extraction values used as reference are provided in Table . (D) Reliability assessment of downsampling-based back-calculation. The relationship between the log-transformed actual matched read counts obtained under 100% extraction and the relative error of the back-calculated 100% equivalent values is shown for each extraction setting. Trend equations were used to estimate approximate matched read ranges corresponding to selected relative error thresholds, which are summarized in Table .

Article Snippet: The feline coronavirus (FCoV) type 2 strain WSU 79-1683 (American Type Culture Collection VR-989) was obtained from the American Type Culture Collection and used in this study.

Techniques: Infection, Generated, Extraction, Derivative Assay, Transformation Assay

Journal: Science Advances

Article Title: RAB5c orchestrates LC3-associated phagocytosis to promote microbicidal function of macrophages

doi: 10.1126/sciadv.adz0196

Figure Lengend Snippet: ( A to F ) BMDMs expressing sh_Ctrl or sh_ Rab5c were stimulated with wild-type (WT; ATCC46645) or Δ pksP A. fumigatus conidia. [(A) and (B)] Confocal images (A) and percentage (B) of LC3 + phagosomes. Insets: DIC of conidia. Scale bar, 10 μm. (C) Percentage of NBT + phagocytes. (D) Percentage of ATP6V1A + phagosomes after 1 hour. [(E) and (F)] Viability of WT (E) and Δ pksP (F) conidia. ( G and H ) Atg16l1 FL and Atg16l1 Δ WD40 BMDMs were stimulated with WT or Δ pksP conidia. Percentage of LC3 + phagosomes (G) and NBT + phagocytes (H). ( I to K ) Viability of WT conidia (I), Δ pksP conidia (J), and WT conidia ± DPI (5 μM) (K) in Atg16l1 FL and Atg16l1 Δ WD40 BMDMs. ( L ) Schematics of A. fumigatus lung infection. Created in BioRender. L. Cunha (2026), https://BioRender.com/l4k0vfu . h, hours. ( M ) Fungal loads in the bronchoalveolar lavage fluid (BAL) samples of infected mice. ( N ) Quantification of albumin in BAL. ( O ) Bright-field images of lung sections stained with Grocott-Gomori’s methenamine silver (top) or hematoxylin and eosin (bottom). Scale bar, 500 μm. Insets: A. fumigatus hyphae. Scale bar, 50 μm. ( P to S ) Quantification of interleukin-6 (IL-6) (P), CCL2 (Q), tumor necrosis factor–α (TNF-α) (R), and IL-1β (S) in BAL. Bars [(B) to (K), (M), (N), and (P) to (S)] represent means of biological replicates (sample or mice), each indicated as a white object. Error bars, ±SEM. Statistical comparison between groups are unpaired Student’s t test [(B) to (J), (M), (N), and (P) to (S)] or ANOVA and Tukey’s multiple comparisons (K) between indicated groups. Data are representative of two [(A) to (D), (G), (H), (J), (K), and (M) to (S)] or three [(E), (F), and (I)] independent experiments.

Article Snippet: Silencing of Rab5c decreased LC3 conjugation to phagosomes containing the A. fumigatus wild-type (WT) strain [American Type Culture Collection (ATCC), 466645] ( ).

Techniques: Expressing, Infection, Staining, Comparison