Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Distribution of segmental duplications (SDs) and bundled long distance interactions in relation to acetylation of H4K8, transcriptional activity and lamina associated domains on human chromosome 7 (derived from IMR90 unless indicated otherwise). A) H4K8 acetylation profile, dark yellow: hyperacetylation of H4K8; blue: hypoacetylation of H4K8. B) the red and blue curve represent RNA-seq read counts/100 kb bin for coding and non-coding RNA, respectively (IMR91L). C) grey areas underlying the two histograms mark lamina associated domains (LADs, Tig3 cells). D) idiogram of chromosome 7, the Williams-Beuren syndrome region is highlighted in yellow beside the idiogram (at 72-74 Mb, hg18). E) transparent blue shading of the idiogram illustrates the inversion-affected segments of chromosome 7 depicted in Figure A-C. Bundled long distance interactions (F) and segmental duplications (G) are depicted in the inner circle; green ribbons: long distance interactions between genomic regions; grey: SDs with sequence similarity <98%; yellow: SDs with sequence similarity 98-99%; orange: SDs with sequence similarity >99%.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Activity Assay, Derivative Assay, RNA Sequencing, Sequencing

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Higher order chromatin organisation and SD localisation around the Williams-Beuren syndrome region. All data are referring to genome release hg19 and are derived from IMR90 unless indicated otherwise. The proximal, central and distal SD clusters (P, C, D) of the 7q11 segment encompassing 4.8 Mb are highlighted in green within the chromosome banding track. A-C) localisation of SDs; colouring according to sequence similarity; grey: <98%, yellow: 98%-99%; orange: >99%; D) genomic interval commonly deleted in WBS and the distal 7q11.23 deletion syndrome; E) topological domains as defined by Dixon et al. ; F) topological domains identified in the corresponding region in mouse after conversion to human hg19. Note that the murine topological domain homologous to sequences deleted in the distal 7q11.23 syndrome is not fully represented due to a break of synteny within this genomic interval. See Figure for details; G-H) heatmap and arc view of CTCF binding sites as detected by ChIA-PET in MCF7; I) number of G4 motifs/100 kb bins; J) average GC-content within 100 kb bins; K) number of Alu repeats/100 kb bin; L) number of structural variants as annotated by Database of Genomic Variance (DGV) , *maximum of 1080 CNVs not shown; M) log2 ratio scores of the LaminB1 DamID Map (Tig3 cells) as reported by Guelen et al. ; N) log2 ratio scores of DNA regions prone to early apoptotic DNA degradation in 20 kb windows, turquoise: degraded DNA segments; O) log2 ratio scores of H4K8 acetylation profile in 20 kb windows, blue: hyperacetylation, grey: hypoacetylation; P) red curve representing the sum of all intrachromosomal interaction counts/bin divided by the median number of interactions for all bins of chromosome 7; Q) percentage of interactions categorised according to their interaction span size ; light grey: <0.5 Mb, grey: 0.5-1 Mb, light blue: 1–5 Mb, light brown: 5–10 Mb, dark grey: 10–25 Mb, black: ≥25 Mb. Gaps in this plot are due to alignment problems of Hi-C data in regions harbouring SDs with high sequence similarity.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Derivative Assay, Sequencing, Binding Assay, ChIA Pet Assay, Hi-C

Journal: BMC Genomics

Article Title: Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7

doi: 10.1186/1471-2164-15-537

Figure Lengend Snippet: Cross-species comparison showing that SDs next to the WBS locus have inserted at topological domain borders. Hi-C interactions and topological domains in the human fetal fibroblast cell line IMR90 are shown in dark green in the upper part as triangle view and bars, respectively. SDs with sequence similarity of 98%-99% and above 99%, respectively, (shown in yellow and orange in the SDs track) coincide with gaps within the Hi-C data. SD distribution and Hi-C data of the corresponding region in mouse are given in the lower part of the image. The position of FKBP6 and WBSCR16 , the human orthologues of the two genes next to the murine topological domain borders are highlighted in green and red, respectively. The intervals commonly affected in WBS and the distal 7q11.23 syndrome are indicated by pale red bars. Note that the region distal to SRRM3 including the distal SD block are homologous to a different mouse chromosome.

Article Snippet: Human fetal lung fibroblast cell lines IMR91L (male) and IMR90 (female) were obtained from the Coriell Institute for Medical Research.

Techniques: Comparison, Hi-C, Sequencing, Blocking Assay

Journal: Nanoscale Advances

Article Title: Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer

doi: 10.1039/d2na00353h

Figure Lengend Snippet: Viability of the normal human lung fibroblast HEL299 cells, treated for 48 h with: (a) – free Dox or D- g -PAAan-Dox in Dox-equivalent concentrations, (b) – free Cis or D- g -PAAan-Cis in Cis-equivalent concentrations; * p < 0.05 compared to free drugs.

Article Snippet: Lung carcinoma human A549 and normal human lung fibroblast HEL299 cell lines were purchased from AddexBio Technologies (San Diego, CA, USA).

Techniques:

Journal: Nanoscale Advances

Article Title: Drug delivery with a pH-sensitive star-like dextran-graft polyacrylamide copolymer

doi: 10.1039/d2na00353h

Figure Lengend Snippet: IC 50 of free drugs and drug-loaded D- g -PAAan nanoparticles on HEL299 cell viability

Article Snippet: Lung carcinoma human A549 and normal human lung fibroblast HEL299 cell lines were purchased from AddexBio Technologies (San Diego, CA, USA).

Techniques:

Journal: BMC Molecular and Cell Biology

Article Title: Intracellular Ca 2+ is not essential for SHH signaling but is promoted by Shh ligand in embryonic fibroblasts

doi: 10.1186/s12860-026-00567-x

Figure Lengend Snippet: Quenching intracellular Ca 2+ does not affect SHH signaling transduction, but high concentrations of extracellular Ca 2+ do. A-C. Response of SHH signaling to manipulations of intracellular and extracellular Ca 2+ . NIH/3T3 cells were stimulated with Shh ( A ), ShhN ( B ), or 100 nM SAG ( C ) for 24 h in the presence of various concentrations of BAPTA or Ca 2+ , and Gli1 protein levels served as a readout for SHH pathway activity. The original Western Blot is provided in Supplementary Fig. . The data were representative of three independent experiments. Statistical analysis: Student’s t-test: ** P < 0.01. D. ATP levels in NIH/3T3 cells treated with SAG and/or Ca 2+

Article Snippet: NIH/3T3 cells (Keygen Biotech, China) were cultured to activate the SHH signaling pathway as described [ ].

Techniques: Transduction, Activity Assay, Western Blot

Journal: BMC Molecular and Cell Biology

Article Title: Intracellular Ca 2+ is not essential for SHH signaling but is promoted by Shh ligand in embryonic fibroblasts

doi: 10.1186/s12860-026-00567-x

Figure Lengend Snippet: Shh ligand promotes Ca 2+ influx after quenching intracellular Ca 2+ with BAPTA. A-B. The changes of intracellular Ca 2+ levels in NIH/3T3 cells treated with Shh conditioned media and/or BAPTA in the SOCE model: imaging (A) and quantification (B) of the changes of intracellular Ca 2+ levels. C-D. Similar to A-B, NIH/3T3 cells were treated with Shh conditioned media and/or Ca 2+ in the SOCE model: imaging (C) and quantification (D) of the changes of intracellular Ca 2+ levels. Statistical analysis: two-way ANOVA

Article Snippet: NIH/3T3 cells (Keygen Biotech, China) were cultured to activate the SHH signaling pathway as described [ ].

Techniques: Imaging

Journal: BMC Molecular and Cell Biology

Article Title: Intracellular Ca 2+ is not essential for SHH signaling but is promoted by Shh ligand in embryonic fibroblasts

doi: 10.1186/s12860-026-00567-x

Figure Lengend Snippet: Smoothened agonist SAG promotes Ca 2+ -induced calcium influx under basal conditions or in the presence of BAPTA. A-B. The changes of intracellular Ca 2+ levels in NIH/3T3 cells treated with SAG in the SOCE model: imaging ( A ) and quantification ( B ) of the changes of intracellular Ca 2+ levels. Statistical analysis: Student’s t -test: * P < 0.05. C-D. Similar to A-B, NIH/3T3 cells were treated with SAG and BAPTA in the SOCE model: imaging ( C ) and quantification ( D ) of the changes of intracellular Ca 2+ levels. Statistical analysis: two-way ANOVA. E-F. Similar to A-B, NIH/3T3 cells were treated with SAG and/or Extra Ca 2+ : Imaging ( E ) and quantification ( F ) of the changes of intracellular Ca 2+ levels in SOCE. Statistical analysis: two-way ANOVA

Article Snippet: NIH/3T3 cells (Keygen Biotech, China) were cultured to activate the SHH signaling pathway as described [ ].

Techniques: Imaging