corynebacterium glutamicum atcc 13032 wild type strain  (ATCC)

Journal: bioRxiv

Article Title: Pseudouridylation landscape across 42 S. cerevisiae cytosolic tRNA isoacceptors via Nanopore direct RNA sequencing

doi: 10.64898/2026.04.28.721490

Figure Lengend Snippet: Subtractive heatmaps comparing Nanopore DRS reference match probabilities of PUS deletion S. cerevisiae cytosolic tRNA to wild-type show changes at expected PUS-modified pseudouridine sites and additional sites. Change in reference match probability is mapped for pus1 Δ (A) and pus7 Δ (B) relative to wild-type. Reference match probability measures the probability that the DRS-called base matches the canonical base in the reference sequence. A positive change in reference match probability (blue) indicates a decrease in miscalls in the PUS deletion relative to WT, while a negative change (red) indicates an increase.

Article Snippet: In brief, purified tRNA (200 ng) from pus1 Δ, pus3 Δ, pus7 Δ, PUS3 D151A, and wild-type budding yeast strains were first hydrolyzed to mononucleotides with 300 U/μg Nuclease P1 (NEB, 100,000 U/mL), 100 mM ammonium acetate, and 100 μM zinc sulfate, in a 10 μL total volume, at 37°C overnight.

Techniques: Modification, Sequencing

Journal: bioRxiv

Article Title: Pseudouridylation landscape across 42 S. cerevisiae cytosolic tRNA isoacceptors via Nanopore direct RNA sequencing

doi: 10.64898/2026.04.28.721490

Figure Lengend Snippet: Total nucleoside LC-MS/MS of pus1 Δ, pus7 Δ, and wild-type S. cerevisiae cytosolic tRNA. Modification abundances of pseudouridine (Ψ), 2-O-methylguanosine (Gm), N2,N2-dimethylguanosine (m 2,2 G), N2-methylguanosine (m 2 G), and 5-methyluridine (m 5 U) for wild-type, pus1 Δ and pus7 Δ tRNA are shown here. Data for all measured modifications are available in Supplemental Table S5. “**” indicates p<0.001 in Dunnett’s multiple comparison test compared to wild-type. Modification / main nucleoside % was calculated as (modification / (canonical base + all modifications to corresponding canonical base))*100.

Article Snippet: In brief, purified tRNA (200 ng) from pus1 Δ, pus3 Δ, pus7 Δ, PUS3 D151A, and wild-type budding yeast strains were first hydrolyzed to mononucleotides with 300 U/μg Nuclease P1 (NEB, 100,000 U/mL), 100 mM ammonium acetate, and 100 μM zinc sulfate, in a 10 μL total volume, at 37°C overnight.

Techniques: Liquid Chromatography with Mass Spectroscopy, Modification, Comparison

Journal: bioRxiv

Article Title: Pseudouridylation landscape across 42 S. cerevisiae cytosolic tRNA isoacceptors via Nanopore direct RNA sequencing

doi: 10.64898/2026.04.28.721490

Figure Lengend Snippet: Subtractive heatmap comparing Nanopore DRS reference match probabilities of pus3 Δ S. cerevisiae cytosolic tRNA to wild-type show changes at expected PUS-modified pseudouridine sites and additional sites. (A) Full subtractive heatmap comparing pus3 Δ and wild-type tRNA. (B) Enlarged subtractive heatmap for positions 36-39. Blue arrows indicate threshold-passing positions annotated to contain i 6 A 37 . Red arrows indicate threshold-passing positions annotated to contain m 1 G 37 . Heatmap scale as in (A). (C) Table showing isoacceptors with a change in reference match probability at position 37 that passed the empirically determined threshold value (Materials and Methods), with canonical base, Modomics-annotated modification, and Pus3-catalyzed modification of the specified isoacceptor. “-” indicates no annotated modification in Modomics.

Article Snippet: In brief, purified tRNA (200 ng) from pus1 Δ, pus3 Δ, pus7 Δ, PUS3 D151A, and wild-type budding yeast strains were first hydrolyzed to mononucleotides with 300 U/μg Nuclease P1 (NEB, 100,000 U/mL), 100 mM ammonium acetate, and 100 μM zinc sulfate, in a 10 μL total volume, at 37°C overnight.

Techniques: Modification

Journal: bioRxiv

Article Title: Pseudouridylation landscape across 42 S. cerevisiae cytosolic tRNA isoacceptors via Nanopore direct RNA sequencing

doi: 10.64898/2026.04.28.721490

Figure Lengend Snippet: Total nucleoside LC-MS/MS and primer extension quantification of tRNA modifications in pus3 Δ, PUS3 D151A and wild-type S. cerevisiae cytosolic tRNA. (A) Modification abundances of pseudouridine (Ψ), 1-methyladenosine (m 1 A), N6-isopentenyladenosine (i 6 A), 1-methylguanosine (m 1 G), and 5-methyluridine (m 5 U) for wild-type, pus3 Δ, and PUS3 D151A tRNA are shown. Data for all measured modifications are available in Supplemental Table S5. “*” indicates p<0.05, “**” indicates p<0.001 in Dunnett’s multiple comparison test compared to wild-type. Modification / main nucleoside % was calculated as (modification / (canonical base + all modifications to corresponding canonical base))*100. (B) IR800-tagged primer specific to LeuCAA. m 1 G 37 and m 2,2 G 26 (modifications causing RT stops) and Ψ 39 catalyzed by Pus3 are labeled. (C) Primer extension assay with three biological replicates of wild-type and pus3 Δ tRNA. “no RNA” negative control reaction contained no added tRNA. RT stops at m 1 G 37 (28 nt) and m 2,2 G 26 (39 nt) are labeled. % m 1 G 37 stop was calculated as (m 1 G 37 intensity / (m 1 G 37 intensity + m 2,2 G 26 intensity))*100. Wild-type and pus3 Δ % stop were compared with a paired one-tailed student’s t-test (p=0.129). The IR800 dye molecule (M.W.= 1163.3 g/mol) causes reverse transcription products to run larger than the ladder oligonucleotides that do not contain this dye. No modifications are known to exist between the 3 end of the primer and position 37. The faint bands just above the primer-only bands may arise from the secondary structure at the beginning of the anticodon stem interrupting reverse transcription.

Article Snippet: In brief, purified tRNA (200 ng) from pus1 Δ, pus3 Δ, pus7 Δ, PUS3 D151A, and wild-type budding yeast strains were first hydrolyzed to mononucleotides with 300 U/μg Nuclease P1 (NEB, 100,000 U/mL), 100 mM ammonium acetate, and 100 μM zinc sulfate, in a 10 μL total volume, at 37°C overnight.

Techniques: Liquid Chromatography with Mass Spectroscopy, Modification, Comparison, Labeling, Primer Extension Assay, Negative Control, One-tailed Test, Reverse Transcription

Journal: bioRxiv

Article Title: Pseudouridylation landscape across 42 S. cerevisiae cytosolic tRNA isoacceptors via Nanopore direct RNA sequencing

doi: 10.64898/2026.04.28.721490

Figure Lengend Snippet: Map of pseudouridines (P) in all 42 S. cerevisiae cytosolic tRNAs based on prior annotations combined with direct RNA sequencing data from this study and our previous study . The enzyme catalyzing P at a given position is denoted by colored boxes. Source of annotation is indicated: P (30 sites): Modomics; P (20 sites): DRS PUS deletion/mutant data from this paper (Pus1, 3, 6, 7, 8) or in (Pus4); P (66 sites): both DRS and Modomics. Italic (11 sites) indicates a Modomics pseudouridine annotation that is present in the tRNA sequence annotation but for which Modomics has not assigned a PUS protein annotation. Two of these eleven sites (GluUUC P 27 and ProUGG P 38 ) also did not exhibit threshold differences in DRS from comparison of wild-type to any of the tested PUS deletions/mutants at the annotated site.

Article Snippet: In brief, purified tRNA (200 ng) from pus1 Δ, pus3 Δ, pus7 Δ, PUS3 D151A, and wild-type budding yeast strains were first hydrolyzed to mononucleotides with 300 U/μg Nuclease P1 (NEB, 100,000 U/mL), 100 mM ammonium acetate, and 100 μM zinc sulfate, in a 10 μL total volume, at 37°C overnight.

Techniques: RNA Sequencing, Mutagenesis, Sequencing, Comparison

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: 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

Journal: Biomaterial Investigations in Dentistry

Article Title: Acrylic-based occlusal device materials – the influence of manufacturing techniques on material properties and the propensity for biofilm formation

doi: 10.2340/biid.v13.45909

Figure Lengend Snippet: Quantification of S. mutans biofilm formation on surfaces of materials from the different workflows. The 24-hour bioreactor approach (A) and the 72-hour culture plate approach (B). Data are presented as mean and SD (error bars). Asterisk (*) indicates a statistically significant difference ( p < 0.05).

Article Snippet: In both experiments, the wild‐type Streptococcus mutans UA159 strain (ATCC 700610) was used as the inoculum.

Techniques: