Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: Relative percentage of bases in each chromHMM ( ; ) category throughout the entire genome ( a ), in fixed or nearly fixed modern human-derived variants ( b ), in active sequences ( c ), and in differentially active sequences ( d ), per cell type. See Discussion for cell-type specificity and enhancer enrichment. ( e ) Histogram of the number of tissues and number of sequences with transcription start site- (TSS) or enhancer-related chromHMM marks for all 14,042 sequences. Tissues and cell types investigated include embryonic stem cells (ESCs), osteoblasts, neural progenitor cells (NPCs), mesenchymal stem cells, monocytes, skin fibroblasts, brain hippocampus, skeletal muscle, heart left ventricle, sigmoid colon, ovary, fetal lung, and liver. Inset shows data for ESC, osteoblast, and NPC only.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Derivative Assay

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: ( a ) Overlap between cell types of active sequences. Super Exact test p-value is shown for the overlap of the three groups. ( b-d ) Enrichment levels of active and repressive histone modification marks within active sequences. Enrichment is computed compared to inactive sequences. The enrichment of H3K27me3 in embryonic stem cells (ESCs) possibly reflects the presence of this mark in bivalent genes, which become active in later stages of development . For confidence intervals, see . ( e ) Enrichment of differentially active sequences in various chromatin-based genomic annotations. Missing circles reflect no differentially active sequences in that category. Stars mark significant enrichments (false discovery rate [FDR] <0.05). ( f ) Violin plots of DNA methylation levels for active (green) vs. inactive (red) sequences in osteoblasts. Methylation levels per sequence were computed as the mean methylation across all modern and archaic human bone methylation samples. The circle marks mean methylation across all sequences in each group. t -test p-value is shown.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Modification, DNA Methylation Assay, Methylation, Sequencing

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: ( a–c ) Violin plots of DNA methylation levels in modern and archaic human bone methylation samples, for differentially active ( a ), promoter differentially active ( b ), and CpG-poor promoter differentially active ( c ) sequences in osteoblasts. Promoter sequences are sequences between 5 kb upstream and 1 kb downstream of a transcription start site (TSS). CpG-poor promoter sequences were defined as the bottom 50% promoter sequences. ( d ) Violin plots of absolute predicted TF binding score difference between modern and archaic sequences. Points show mean.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: DNA Methylation Assay, Methylation, Binding Assay

Journal: eLife

Article Title: The cis -regulatory effects of modern human-specific variants

doi: 10.7554/eLife.63713

Figure Lengend Snippet: (a–c) Expression fold-change vs. predicted TF binding fold-change for each sequence. Positive scores represent increased binding in the modern sequence. Parentheses show number of points in each quadrant with a score difference >0. ( d ) Pearson’s correlation between differential expression and predicted differential binding affinity. Only significant TFs (false discovery rate [FDR] ≤0.05, ) are shown for osteoblasts (yellow) and neural progenitor cells (NPCs) (red). ( e ) Expression fold-change vs. predicted TF binding fold-change for ZNF281 in NPCs. Pearson’s r and p-value are shown. ( f ) Enriched Gene Ontology terms for embryonic stem cells (ESCs) (blue), osteoblasts (yellow), and NPCs (red). ( g ) Expression fold-change of differentially active sequences compared to the cis -regulatory expression fold-change between human and chimpanzee of genes associated with these sequences. cis -regulatory expression changes were taken from hybrid human-chimpanzee induced pluripotent stem cells (iPSCs) . ( h ) RT-qPCR validation of NPCs at passage 1 (pink) and passage 10 (red). Expression levels are normalized to HPRT expression.

Article Snippet: Human fetal osteoblasts were purchased from Cell Applications Inc (406 K-05f, tested negative for mycoplasma) and were maintained in Osteoblast Growth Medium (Cell Applications Inc).

Techniques: Expressing, Binding Assay, Sequencing, Quantitative Proteomics, Quantitative RT-PCR, Biomarker Discovery

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 1. Phenotyping of human cord blood stem cell-derived cardiomyocytes. (A) Cardiomyocytes were cultured in chamber slides, permeab- ilized, and treated with rhodamine-labeled secondary antibody. (B) 4,6-Diamidino-2-phenylindole nuclear stain (B). (C) cTnI primary antibody and rhodamine-labeled secondary antibody. (D) A composite image created by superimposing the images in panels B and C.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Derivative Assay, Cell Culture, Labeling, Staining

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 2. Effect of the B40 aptamer in comparison to the effects of a panel of 17 ARVs on the viability of human cardiomyocytes and PBMCs. Human cord blood stem cell-derived cardiomyocytes or freshly isolated PBMCs were seeded at a density of 20,000 cells/well in 96-well plates and exposed to the respective ARVs at a concentration equivalent to the Cmax shown in Table 1 or the B40 aptamer at 2 M. All experiments were done in triplicate and were independently re- peated twice. ATP levels were measured as a correlate of cell viability after 7 days of exposure by relating the RLU of treated cells to the RLU of untreated cells. The results were normalized and expressed as the percent cell death for the treated cell samples by comparison to the number of untreated cells. The data on the graph show the means, and the error bars represent the standard deviations for three replicates in two sets of independent experiments. ARVs whose toxicity was statis- tically different from that of the untreated controls, as determined by the t test, are indicated as follows: *, P 0.01; **, P 0.001; ***, P 0.0001.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Comparison, Derivative Assay, Isolation, Concentration Assay

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 3. Caspase 3/7 activity in cardiomyocytes (A) and PBMCs (B) upon exposure to ARVs. Cells seeded at a density of 50,000 cells/well were exposed to EFZ, ABC, TDF, RTV, IND, T20, or the B40 aptamer at the Cmax for 1, 4, and 7 days. No statistically significant increases in caspase 3/7 activity were observed for any ARV, including the B40 aptamer, in cardiomyocytes or PBMCs compared to the ac- tivity in untreated control cells. A statistically significant decrease in caspase 3/7 activity was observed at least at day 4 and 7 in cardiomy- ocytes (A) and PBMCs (B) treated with EFV, ABC, TDF, and RTV compared to the activity in untreated control cells, as determined by the t test. *, P 0.002; **, P 0.0002. The data on the graphs represent the means, and the error bars represent the standard devi- ations for three replicates in two sets of independent experiments.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Activity Assay, Control

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 4. MAO A and B enzyme modulation by the B40 aptamer and T20 in cardiomyocytes (A and C) and PBMCs (B and D). Cells were incubated in triplicate with the serially diluted test molecule at a maximum concentration of 2 M for 2 h. A cell lysate was incubated with MAO A or B substrate for 1 h, followed by the addition of detection reagent, and the resulting luminescence signal was quantified in a luminometer. The no-treatment control was used as the baseline for maximum enzyme activity. No change in enzyme activity was detected for either MAO A or MAO B in the presence of the B40 aptamer and T20 for both cardiomyocytes and PBMCs. However, there was a dose-dependent inhibition of MAO A by clorgyline and MAO B by deprenyl, which are well-documented inhibitors of MAO A and MAO B, respectively, indicating the presence and activity of both enzymes in human cardiomyocytes and PBMCs. Enzyme activity was calculated by relating the RLUs of untreated control cells to that of the treated cells as a percentage. The data on the graphs represent the means, and the error bars represent the standard deviations for three replicates in two sets of independent experiments.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Incubation, Concentration Assay, Control, Activity Assay, Inhibition

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 5. Effects of the B40 aptamer and T20 on CYP3A4 enzyme activity in cardiomyocytes (A) and PBMCs (B). Cells were seeded at a density of 20,000 cells/well and exposed to the respective test molecule in triplicate for 2 days at serially diluted concentrations. The overlay medium was removed, and fresh medium containing a luciferin luminogenic substrate for the CYP3A4 enzyme was added. After 4 h of incubation, the luciferin detection reagent was added and the resulting luminescence signal was quantified in a luminometer. The no-treatment control was used as the baseline for maximum enzyme activity, and RTV, a known inhibitor of CYP3A4 (36, 56), was used as a positive control. The data on the graphs represent the means, and the error bars represent the standard deviations for three replicates in two sets of independent experiments.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Activity Assay, Incubation, Control, Positive Control

Journal: Antimicrobial Agents and Chemotherapy

Article Title: Cytotoxicological Analysis of a gp120 Binding Aptamer with Cross-Clade Human Immunodeficiency Virus Type 1 Entry Inhibition Properties: Comparison to Conventional Antiretrovirals

doi: 10.1128/aac.01502-08

Figure Lengend Snippet: FIG. 6. Effects of the B40 aptamer and T20 on mitochondrial tox- icity, as measured by determination of the mtDNA/nDNA ratio in cardiomyocytes and PBMCs. Cardiomyocytes and PBMCs were ex- posed to 2 M B40 aptamer, T20, or ddC in triplicate for 7 days. The relative amounts of nDNA and mtDNA were quantified by real-time quantitative PCR amplification of the CCOI nuclear gene and the ASPOLG mitochondrial gene, respectively. The data were extrapo- lated from a standard curve relating the cycle numbers to the relative DNA concentration. The mtDNA/nDNA ratio for the untreated sam- ple was arbitrarily set equal to 1.0. Only the ddC-treated cells showed a statistically significant decrease in the mtDNA/nDNA ratio com- pared to that for the untreated control, as determined by a t test and as indicated as follows: *, P 0.001; **, P 0.0001. The data on the graph represent the means, and the error bars represent the standard deviations for three replicates in two independent experiments.

Article Snippet: The human cord blood stem cell-derived cardiomyocytes were purchased from Celprogen.

Techniques: Real-time Polymerase Chain Reaction, Concentration Assay, Control

Journal: PLOS ONE

Article Title: Evaluation of decellularization process for developing osteogenic bovine cancellous bone scaffolds in-vitro

doi: 10.1371/journal.pone.0283922

Figure Lengend Snippet: Bar charts indicate comparison between DCC scaffold vs DCC scaffold + cells and DMB scaffolds vs DMB scaffold + cells by direct method (a). Bar charts indicate comparison between DMB conditioned media (CM) and DCC conditioned media (CM) vs complete culture media (Control) by indirect method (b). *p<0.05 is indicated. n = 4; CM: conditioned media. (c). HOB cells seeded on DMB and DCC scaffolds showing optimum cell attachment by DAPI staining. (i & iii) DMB scaffolds and (ii & iv) DCC scaffolds; images were captured by fluorescence and confocal microscopy, respectively. Scanning electron micrograph of HOB cells seeded onto DMB (d) and DCC (e) scaffolds. The osteoblast shows a healthy morphology residing on the ECM with evidence of filopodia spread (red arrows).

Article Snippet: Human osteoblast cells (HOB) used for biocompatibility evaluation were obtained from Addexbio (Cat no: P0004010; USA).

Techniques: Comparison, Control, Cell Attachment Assay, Staining, Fluorescence, Confocal Microscopy

Journal: PLOS ONE

Article Title: Evaluation of decellularization process for developing osteogenic bovine cancellous bone scaffolds in-vitro

doi: 10.1371/journal.pone.0283922

Figure Lengend Snippet: Photomicrographs of HOB cells stained with Alizarin Red S. HOB cells showed increased mineralized nodules in osteogenic medium (OS + ) compared to cells without supplements (OS - ). More significant mineralization was seen by day 14 (a). Quantification of alizarin Red S stained mineralized nodules in human osteoblast cells seeded on DMB and DCC scaffolds grown in the presence or absence of osteogenic induction media at days 7 and 14 in comparison to cells alone is shown; p<0.001 is indicated). The absorbance of the extracted Alizarin dye was measured at 405 nm. Data presented as mean ± SEM (n = 6) (b). Quantification of Alizarin Red S staining in osteoblast cell-seeded DMB and DCC scaffolds on day 14 in the presence and absence of osteogenic supplements. Data presented as mean ± SEM (n = 4) (c); p<0.001 is indicated.

Article Snippet: Human osteoblast cells (HOB) used for biocompatibility evaluation were obtained from Addexbio (Cat no: P0004010; USA).

Techniques: Staining, Comparison

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Preinvestigation of PRP and PRF for in-vitro addition. The effect of PRP and PRF were examined in different concentrations to fibroblasts ( A ) and osteoblasts ( B ) by real- time cell analysis.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: In Vitro, Cell Analysis

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Representative photographs of cell migration using the scratch assay. The effect of ZA, PRP, PRF and their combination on the migration of fibroblasts ( A ) and osteoblasts ( B ) were examined (PC = positive control; NC = negative control; ZA = zoledronic acid).

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: Migration, Wound Healing Assay, Positive Control, Negative Control

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Percentage of closure of the scratch area in fibroblasts ( A ) and osteoblasts ( B ) in the different groups (1.0 = 100% coverage). Significant difference ( p < 0.05) is marked with *.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques:

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Migration of fibroblasts and osteoblasts using the scratch assay.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: Migration

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Effects of PRP, PRF, ZA and their combinations on the viability of human gingival fibroblasts ( A ) and osteoblasts ( B ) assessed by MTT assay. Significant difference ( p < 0.05) is marked with *.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: MTT Assay

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Results of the MTT test performed on fibroblasts and osteoblasts at different times.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: MTT Assay

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: Cell proliferation assessed by real-time cell analysis for fibroblasts ( A ) and osteoblasts ( B ) in the different groups over a period of 72 h. The values are the median of the measured cell index. Significant difference ( p < 0.05) is marked with *.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: Cell Analysis

Journal: Scientific Reports

Article Title: Positive impact of Platelet-rich plasma and Platelet-rich fibrin on viability, migration and proliferation of osteoblasts and fibroblasts treated with zoledronic acid

doi: 10.1038/s41598-019-43798-z

Figure Lengend Snippet: cell proliferation of fibroblasts and osteoblasts using the Real-time cell analysis assay.

Article Snippet: Primary human gingival fibroblasts (hGF) and human osteoblasts (hOB) were purchased from Provitro® (Berlin, Germany).

Techniques: Cell Analysis