Journal: Orphanet Journal of Rare Diseases

Article Title: Impaired osteoblast and osteoclast function characterize the osteoporosis of Snyder - Robinson syndrome

doi: 10.1186/s13023-015-0235-8

Figure Lengend Snippet: Characterization of the bone and osteoblast pathology. A . Photograph of the bone biopsy. B . Steady state SMS mRNA levels relative to GAPDH expression in cultured fibroblasts and osteoblasts. The patient’s cells did not differ significantly from controls. Data were derived by qRT-PCR analysis of 3 independent extractions of total RNA. C . Immunoblot showing steady state SMS protein expression in patient and control osteoblasts. ß-tubulin is shown as a loading control. D . Graph showing steady state SMS protein levels in the patient and control hBMSCs relative to ß-tubulin levels; there was no significant difference. The data are based on 3 independent experiments for each cell line. E - J . Immunofluorescent detection of SMS protein subcellular distribution in unaffected (E-G) and Patient II-1 (H-J) hBMSCs. SMS protein is shown in red and the nucleus is shown in blue. K . Graph quantifying immunoblot detected steady state SMS protein levels in the cytoplasm and nuclei of patient and control hBMSCs. The cytoplasmic expression was normalized to β-tubulin expression and the nuclear expression to p84 expression. L . Polyamine quantification in fibroblasts and osteoblasts. Note that the patient hBMSCs have a more striking imbalance of spermidine and spermine levels than do the patient fibroblasts, * p < 0.05, *** p < 0.005. M . Osteogenic potential of bone marrow stromal cells (hBMSCs) isolated from Patient II-1 sample is markedly lower than that of an unaffected control (cnt). The hBMSCs were seeded in triplicates (6x10 4 /12-well) and either kept untreated (-) or treated (+) with osteogenic differentiation media (see ) for 18 days. After the treatment, cells were fixed and were stained with Alizarin Red S to check for calcium deposition, a marker of osteogenic differentiation.

Article Snippet: We also measured spermine and spermidine levels in cultured human bone marrow stromal cells (hBMSCs) and fibroblasts using the Biochrom 30 polyamine protocol and assessed the osteogenic potential of hBMSCs.

Techniques: Expressing, Cell Culture, Derivative Assay, Quantitative RT-PCR, Western Blot, Control, Isolation, Staining, Marker

Journal: BMC Nephrology

Article Title: Dissolved molecular hydrogen (H 2 ) in Peritoneal Dialysis (PD) solutions preserves mesothelial cells and peritoneal membrane integrity

doi: 10.1186/s12882-017-0741-0

Figure Lengend Snippet: Representative histological findings in the peritoneum: Masson and immunohistochemistry staining in PD and H 2 PD groups. Mesenchymal marker: vimentin; proliferative marker: Ki-67; apoptosis marker: M30 CytoDeath; total macrophage marker: CD68+; M1 macrophage: CD80+; M2 macrophage: CD163+

Article Snippet: Immunohistochemical analysis was performed using monoclonal antibodies against the mesenchymal marker vimentin (Santa Cruz Biotechnology Inc., Dallas, TX), proliferative marker Ki-67 (Novus Biologicals, CO), apoptosis marker M30 CytoDeath (PEVIVA, Sundbyberg, Sweden), total macrophage CD68 mouse anti-rat monoclonal (ED1) antibody (LSBio, Seattle, WA), M1 macrophage CD80 mouse monoclonal antibody (Origene Technologies Inc., Rockville, MD), and M2 macrophage CD163 mouse monoclonal antibody (Leica Biosystems, Nussloch, Germany).

Techniques: Immunohistochemistry, Staining, Marker

Journal: BMC Nephrology

Article Title: Dissolved molecular hydrogen (H 2 ) in Peritoneal Dialysis (PD) solutions preserves mesothelial cells and peritoneal membrane integrity

doi: 10.1186/s12882-017-0741-0

Figure Lengend Snippet: Quantitative analysis of peritoneal thickness and immunohistochemical staining of the peritoneum in PD and H 2 PD groups. Peritoneal thickness ( a ), and immunostainings of mesenchymal marker: vimentin ( b ), proliferative marker: Ki-67 ( c ), apoptosis marker: M30 CytoDeath ( d ), and total macrophage marker: CD68+, M1 macrophage: CD80+, and M2 macrophage: CD163+ ( e ), and ratio of M1 /M2 (positive cells number per field) ( f ). * p < 0.05

Article Snippet: Immunohistochemical analysis was performed using monoclonal antibodies against the mesenchymal marker vimentin (Santa Cruz Biotechnology Inc., Dallas, TX), proliferative marker Ki-67 (Novus Biologicals, CO), apoptosis marker M30 CytoDeath (PEVIVA, Sundbyberg, Sweden), total macrophage CD68 mouse anti-rat monoclonal (ED1) antibody (LSBio, Seattle, WA), M1 macrophage CD80 mouse monoclonal antibody (Origene Technologies Inc., Rockville, MD), and M2 macrophage CD163 mouse monoclonal antibody (Leica Biosystems, Nussloch, Germany).

Techniques: Immunohistochemical staining, Staining, Marker

Journal: BMC Nephrology

Article Title: Dissolved molecular hydrogen (H 2 ) in Peritoneal Dialysis (PD) solutions preserves mesothelial cells and peritoneal membrane integrity

doi: 10.1186/s12882-017-0741-0

Figure Lengend Snippet: Comparison of Fe-PD and Fe-H 2 PD groups. Representative findings of Masson and immunohistochemical staining (CD68) ( a ), and quantitative analysis of peritoneal morphology and immunohistochemical staining of the peritoneum in the respective groups ( b - g ) are shown. Peritoneal thickness ( b ), ratio of shed cells in the peritoneal surface ( c ), immunostainings of mesenchymal marker: vimentin ( d ), apoptosis marker: M30 CytoDeath ( e ), proliferative marker: Ki-67 ( f ), and total macrophage marker: CD68+, M1 macrophage: CD80+, and M2 macrophage: CD163+ ( e ), respectively. * p < 0.05

Article Snippet: Immunohistochemical analysis was performed using monoclonal antibodies against the mesenchymal marker vimentin (Santa Cruz Biotechnology Inc., Dallas, TX), proliferative marker Ki-67 (Novus Biologicals, CO), apoptosis marker M30 CytoDeath (PEVIVA, Sundbyberg, Sweden), total macrophage CD68 mouse anti-rat monoclonal (ED1) antibody (LSBio, Seattle, WA), M1 macrophage CD80 mouse monoclonal antibody (Origene Technologies Inc., Rockville, MD), and M2 macrophage CD163 mouse monoclonal antibody (Leica Biosystems, Nussloch, Germany).

Techniques: Immunohistochemical staining, Staining, Marker

Journal: BMC Biology

Article Title: A systematic sequencing-based approach for microbial contaminant detection and functional inference

doi: 10.1186/s12915-019-0690-0

Figure Lengend Snippet: Overall structure of the proposed pipeline and results of the performance assessment. a Schematic representation of the proposed pipeline that executes rigorous read alignment with a large-scale genome database. b FDR distribution in the reversion tests considering falsely mapped reads to other species or to other genera. Particular genera, including Raoultella , Shigella , and Kluyvera , are difficult to distinguish genomically. c Comparative analysis for the effects of uniq-genus-hits and weighted multi-genera-hits in quantification. “Total mapped” represents the sum of uniq-genus-hits (Unique and Unambiguous) and multi-genera-hits (Multiple and Ambiguous). “Weighted” represents the adjusted “Total mapped” by our scoring scheme. d Correlations between the detection quantification and spike-in concentration assayed by DNA-seq (0-day cultured hPDL-MSCs with antibiotics). e RPMH differences among three NGS protocols in Mycoplasma spike-in detections (3-day cultured hPDL-MSCs)

Article Snippet: We performed the same analysis by incorporating the Myco(+) human bone marrow MSCs (hBM-MSCs) used in Fig. a and Myco(−) hBM-MSCs (GSE90273).

Techniques: Concentration Assay, DNA Sequencing, Cell Culture

Journal: BMC Biology

Article Title: A systematic sequencing-based approach for microbial contaminant detection and functional inference

doi: 10.1186/s12915-019-0690-0

Figure Lengend Snippet: Results of the Mycoplasma prevalence analysis and the functional impacts on host cells. a Twenty-two out of 432 public RNA-seq datasets contained significant Mycoplasma -mapped reads (red-colored bar) that were normalized to RPMHs (blue-colored line); the x -axis labels are colored black for DRA001846, gray for IHBM2, blue for ENCODE, and red for Mycoplasma -positive samples. b Gene expression correlation plots between Mycoplasma -positive (Myco+) and Mycoplasma -negative (Myco-) MSCs; Myco(+) hPDL-MSCs are Mycoplasm a spike-in cells (2000 CFU × 7 species, 3 days cultured without antibiotics), FPKMs were transformed onto the log 10 scale by adding one, and the black-labeled genes are the 13 genes listed in d . c Highly enriched Gene Ontology terms and Reactome pathways ( q value after Bonferroni correction < 0.001). d Venn diagram showing unique or shared differentially upregulated genes (DUGs) in MSCs, including 13 out of 967 DUGs unique to Myco(+) MSCs. e Expression levels of the 13 genes in Myco(+) ESCs and MSCs; the values are expressed as relative TPM (transcripts per million)

Article Snippet: We performed the same analysis by incorporating the Myco(+) human bone marrow MSCs (hBM-MSCs) used in Fig. a and Myco(−) hBM-MSCs (GSE90273).

Techniques: Functional Assay, RNA Sequencing, Gene Expression, Cell Culture, Transformation Assay, Labeling, Expressing

Journal: BMC Biology

Article Title: A systematic sequencing-based approach for microbial contaminant detection and functional inference

doi: 10.1186/s12915-019-0690-0

Figure Lengend Snippet: Inference of DUGs associated with multiple contaminants in Myco(+) DG75 samples. a Expression profile of 967 DUGs unique to Myco(+) MSCs. b Contamination profile with MSC, ESC, and DG-75 samples; the x -axis labels are colored black for Myco(−) and red for Myco(+). c Schematic representation of module identification from two input profiles by the jNMF algorithm. d An example showing the module that captured genes and contaminants co-elevated in a DG-75 sample. e Network representation of the association between genes and contaminants co-elevated in the seven DG-75 samples; GO:0010941 is the enriched GO term in the genes found in at least four DG-75 samples ( p = 3.76e−3). f Expression profiles of the 33 genes involved in the biological process “regulation of cell death”, DG75_1 (GSM1197380), DG75_2 (GSM1197385), DG75_3 (GSM1197386), DG75_4 (GSM1197381), DG75_5 (GSM1197382), DG75_6 (GSM1197383), DG75_7 (GSM1197384), NB_1 (GSM2225743), and NB_2 (GSM2225744)

Article Snippet: We performed the same analysis by incorporating the Myco(+) human bone marrow MSCs (hBM-MSCs) used in Fig. a and Myco(−) hBM-MSCs (GSE90273).

Techniques: Expressing