Journal: BMC Genomics

Article Title: The role of nitric oxide during embryonic wound healing

doi: 10.1186/s12864-019-6147-6

Figure Lengend Snippet: Production of NO during wound healing and regeneration. ( a ) Control embryos at stage 26 were injured using a needle, or tails of tadpoles at stage 41 were amputated and incubated in media with DAF-2DA solution for 15 minutes, fixed and imaged. ( b ) NO is produced in the first two layers of cells around wound edge (Scale bar = 20 μm). ( c , d ) NO is produced mainly during first 15 minutes after injury in embryos at stage 26 (Scale bar = 100 μm, five replicates, mean with standard deviation, One-way ANOVA Dunnett’s multiple comparisons test) ( e , f ) and after amputation in embryos at stage 41. (Scale bars = 200 μm, three replicates, mean with standard deviation, One-way ANOVA Dunnett’s multiple comparisons test) ( g ) NO is not produced after injury at stage 1 and stage 5, but NO is produced after injury at stage 8 (blastula), stage 11 (gastrula), stage 14 (early neurula) and stage 20 (late neurula) (Scale bar = 500 μm). CTF – corrected total fluorescence, RFU – relative fluorescent unit, pw – post wounding, pa – post amputation **** - p < .0001, * - p < .05, n.s. - p > .05

Article Snippet: The statistical significance was calculated relative to the control using GraphPad Prism 7 One-way ANOVA with Dunnett’s multiple comparisons test.

Techniques: Control, Incubation, Produced, Standard Deviation, Fluorescence

Journal: BMC Genomics

Article Title: The role of nitric oxide during embryonic wound healing

doi: 10.1186/s12864-019-6147-6

Figure Lengend Snippet: Changes in gene expression during wound healing after inhibition of NO production. ( a ) Graphical description of RNA-Seq experiment comparing control and NO inhibited embryonic wound healing. Only the part marked by red rectangle was collected and used for RNA isolation and sequencing. ( b - g ) DEGs, which were identified in RNA-Seq, were grouped based on their expression profile relatively to 0 minutes and GO analysis was performed. ( b , d , f ) Expression profiles of genes are representative of the z-score of the regularized log transformation of the normalized counts. ( c , e , g ) Genes with annotation and human homolog were used for GO analysis. Numbers of analysed genes are in the table together with the representative GO terms for each group. ( h ) RNA-Seq result of lep expression was verified ( i ) using RT-qPCR, separately for nos1 -MO and nos3 -MO. ( j ) Similarly, RNA-Seq result of fos expression was verified using ( k ) RT-qPCR (data are normalized to 0 minutes pw in controls, three replicates, geometric mean with geometric standard deviation, two-sided t-test from log2 values of relative expression between inhibited samples and control in 120 minutes pw), and ( l ) in situ hybridization. Site of injury is marked with a star and the signal where fos is expressed is circled by dot line (Scale bar = 100 μm) (M) Intensity of blue signal around site of injury were measured (one-way Anova, Dunnett’s multiple comparisons test, minimum 8 replicates). **** - p < .0001, ** - p < .01, * - p < .05, n.s. - p > .05 DEGs – differentially expressed genes, pw – post wounding, RIU – relative intensity unit

Article Snippet: The statistical significance was calculated relative to the control using GraphPad Prism 7 One-way ANOVA with Dunnett’s multiple comparisons test.

Techniques: Gene Expression, Inhibition, RNA Sequencing, Control, Isolation, Sequencing, Expressing, Transformation Assay, Quantitative RT-PCR, Standard Deviation, In Situ Hybridization

Journal: BMC Genomics

Article Title: The role of nitric oxide during embryonic wound healing

doi: 10.1186/s12864-019-6147-6

Figure Lengend Snippet: Monitoring of phenotype changes during wound healing in embryos with inhibited NO production. ( a , b , c ) Control embryos, embryos with inhibited production of NO using TRIM 1 hour before injury and embryos injected with mixture of nos1 + nos3 - MO were injured at stage 26 using forceps or needle in the middle and ventral side. ( d ) Laminin layer was visualized at 180 minutes and 360 minutes pw and ends of the laminin layer are marked by a triangle. Formation of “blob” in TRIM embryos is marked by arrow (Scale bar = 100 μm). ( e ) Staining of β- catenin 360 minutes pw (Scale bar = 100 μm). ( f ) Brightfiled image of wound site in 180 minutes pw (Scale bar = 100 μm). ( b , g ) Actin at 30, 60 and 180 minutes pw visualized using green fluorescent phalloidin. Breaks in actin layer are marked by arrow (Scale bar = 100 μm). ( c , h ) Collagen staining at 60 minutes pw. The beginning of the wound is marked by a red triangle. A red arrow marks the end of the collagen layer, while the end of the wound site is marked by a red star. (Scale bar = 100 μm, measurement of coverage of collagen in wound was made from at least six embryos per condition and at least five slices per embryo, one-way anova, Dunnett’s multiple comparisons test). ( i ) Spatial expression of two matrix metalloproteinases mmp7 and mmp9 was visualized by in situ hybridization in time 360 minutes pw (Scale bars = 500 μm). ( j ) RT-qPCR comparison of temporal expression profiles of mmp1 , mmp8 , mmp7 and mmp9 (data are normalized to 0 minutes pw in controls, three replicates, geometric mean with geometric standard deviation, two-sided ttest from log2 values of relative expression between 360 minutes and 0 minutes). **** - p < .0001, *** - p < .001, ** - p < .01, n.s. - > .05 pw – post wounding

Article Snippet: The statistical significance was calculated relative to the control using GraphPad Prism 7 One-way ANOVA with Dunnett’s multiple comparisons test.

Techniques: Control, Injection, Staining, Expressing, In Situ Hybridization, Quantitative RT-PCR, Comparison, Standard Deviation

Journal: bioRxiv

Article Title: 3D printed bioelectronic scaffolds with soft tissue-like stiffness

doi: 10.1101/2024.07.19.604334

Figure Lengend Snippet: A) Representative images of samples after post-treatment. B-E) Post-treatment with solvents or acids influences the B) elastic modulus, C) volumetric swelling (percentage relative to as-fabricated hydrogels, without treatment), D) water fraction and E) electronic conductivity of hydrogels. F-G) X-ray S 2p photoelectron spectra of treated and as-fabricated hydrogels indicates a decrease in PSS after all treatments. The de-convoluted profiles were fitted with asymmetric functions. Mean and standard deviation presented. Quantification of PSS/PEDOT ratio calculated from a comparison of the area under the curves of the XPS fits. N≥4. One-way analysis of variance (ANOVA) and Dunnett’s multiple comparison test performed. ****P≤0.0001, ***P≤0.001, **P≤0.01, *P≤0.05, Non-Significant (NS) P>0.05. H) Pearson’s correlation heatmap showing the correlation between PSS/PEDOT ratio (P), water fraction (W), elastic modulus (M) and conductivity (C). I) Survey of recent literature that report modulus and conductivity of 3D printed PEDOT:PSS hydrogels. High conductivity often leads to stiffness values outside the physiological range. The present study joins very few others able to meet satisfactory conductivity with elastic moduli representing soft tissues.

Article Snippet: For statistical analysis, ordinary one-way ANOVA with Sıdak’s or Dunnett’s multiple comparison tests were performed with GraphPad Prism.

Techniques: Standard Deviation, Comparison

Journal: bioRxiv

Article Title: 3D printed bioelectronic scaffolds with soft tissue-like stiffness

doi: 10.1101/2024.07.19.604334

Figure Lengend Snippet: A) Representative strain amplitude sweep of treated and untreated hydrogels to determine the storage modulus (10 rad⋅s -1 , 25 °C). B) Storage modulus obtained from A. One-way analysis of variance (ANOVA) and Dunnett’s multiple comparison test performed. ****P≤0.0001, ***P≤0.001, **P≤0.01, *P≤0.05, Non-Significant (NS) P>0.05. C) Post-treatment causes a decrease in dimensions. The shrinkage occurs nearly isotopically ( xy/z = 0.94 – 1.16). N≥4. Mean and standard deviation presented.

Article Snippet: For statistical analysis, ordinary one-way ANOVA with Sıdak’s or Dunnett’s multiple comparison tests were performed with GraphPad Prism.

Techniques: Comparison, Standard Deviation

Journal: Frontiers in Immunology

Article Title: The Smac Mimetic BV6 Improves NK Cell-Mediated Killing of Rhabdomyosarcoma Cells by Simultaneously Targeting Tumor and Effector Cells

doi: 10.3389/fimmu.2017.00202

Figure Lengend Snippet: Natural killer (NK) cells tolerate higher concentrations of Smac mimetics (SM) than RH30 cells . (A) RH30 and (B) NK cells were challenged with increasing doses of SM (0, 2.5, 5, 10, 20, 30, and 50 μM). The percentage of viable cells was determined with a life–dead stain (DAPI) in flow cytometry after 24 and 48 h. (C) NK cells were isolated and cultured in medium containing increasing doses of SM in addition to IL-2. On day 3, 6, and 9, they were fed with fresh medium including both additives and their proliferative behavior was tracked through cell counts. The determined cell numbers were considered in relation to the absolute number of cells on day 0. Data concerning the impact of SM on RMS cells are always depicted in orange (RH30) or red (RD), and NK cells in green color. Three individual experiments were performed for each setting ( n = 3). Statistical analysis with repeated measures one-way ANOVA + Dunnett’s multiple comparison, * p < 0.05, ** p < 0.01, *** p < 0.001, **** p < 0.0001, each referred to 0 μM.

Article Snippet: The statistical analyses of cytotoxicity assays as well as SM-induced changes in NK cell surface markers and viability experiments were performed using the repeated measures one-way ANOVA with Dunnett’s multiple comparison in GraphPad Prism 6 (Inc. LA JOLLA, CALIFORNIA, USA).

Techniques: Staining, Flow Cytometry, Isolation, Cell Culture, Comparison

Journal: Frontiers in Immunology

Article Title: The Smac Mimetic BV6 Improves NK Cell-Mediated Killing of Rhabdomyosarcoma Cells by Simultaneously Targeting Tumor and Effector Cells

doi: 10.3389/fimmu.2017.00202

Figure Lengend Snippet: Pretreatment with SM effects both RH30 and NK cells . (A) SM sensitize RH30 cells toward NK cell mediated killing. RH30 cells were pretreated with 0, 5, or 10 μM SM for 24 h prior to being used as targets for IL-2-stimulated NK cells on day six of culture (as depicted in the scheme on the right-hand side). The cytotoxicity assay was repeated with NK cells of four different donors ( n = 4). E:T ratio = 10:1, coculture time 4 h. (B) SM increase the cytotoxic potential of NK cells. NK cells were cultured with different doses of SM (0, 5, and 10 μM) in addition to IL-2 for 7 days (as depicted in the scheme on the right-hand side). On day seven, cytotoxicity assays were performed using untreated RH30 cells as targets. The experiment was repeated with NK cells from seven different donors ( n = 7). E:T ratio = 10:1, coculture time 16 h. Statistical analysis through repeated measures one-way ANOVA + Dunnett’s multiple comparison, *** p < 0.001, **** p < 0.0001, each referred to 0 μM.

Article Snippet: The statistical analyses of cytotoxicity assays as well as SM-induced changes in NK cell surface markers and viability experiments were performed using the repeated measures one-way ANOVA with Dunnett’s multiple comparison in GraphPad Prism 6 (Inc. LA JOLLA, CALIFORNIA, USA).

Techniques: Cytotoxicity Assay, Cell Culture, Comparison