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

Journal: iScience

Article Title: TGF-β1 promotes osteogenesis of mesenchymal stem cells via integrin mediated mechanical positive autoregulation

doi: 10.1016/j.isci.2024.110262

Figure Lengend Snippet:

Article Snippet: Human bone marrow MSCs (mesenchymal stem cells derived from bone marrow of adults) were purchased from Cyagen Biosciences Inc. (HUXMA-01001; Guangzhou, China) and cultured in MSCs specific growth medium (HUXMA-90011 and HUXMA-80011; Cyagen, China) at 37°C with 5% CO 2 according to manufacturer’s instructions.

Techniques: Recombinant, Enzyme-linked Immunosorbent Assay, RNA Extraction, Real-time Polymerase Chain Reaction, Software

Journal: International Journal of Nanomedicine

Article Title: Mesoporous bioactive glass surface modified poly(lactic-co-glycolic acid) electrospun fibrous scaffold for bone regeneration

doi: 10.2147/IJN.S82543

Figure Lengend Snippet: Cell proliferation of hMSCs incubated on samples after 1, 3 and 5 days. Notes: P2, P4, or P8 represents the PLGA scaffold coated by MBG precursor solution for 2, 4, or 8 times, respectively. P0 represents the unmodified PLGA scaffold. Abbreviations: hMSCs, human mesenchymal stem cells; MBG, mesoporous bioactive glass; PLGA, poly(lactic-co-glycolic acid).

Article Snippet: Human mesenchymal stem cells (hMSCs) (ScienCell Research Laboratories, San Diego, CA, USA) were cultured in Minimum Essential Medium Eagle-alpha modification (α-MEM) culture medium supplemented with 20% fetal bovine serum (FBS), 1% penicillin (100 U/mL), and streptomycin sulphate (100 μg/mL) (GibcoBRL, Grand Island, NY, USA).

Techniques: Incubation

Journal: International Journal of Nanomedicine

Article Title: Mesoporous bioactive glass surface modified poly(lactic-co-glycolic acid) electrospun fibrous scaffold for bone regeneration

doi: 10.2147/IJN.S82543

Figure Lengend Snippet: ALP activity and ALP staining assay. Notes: ( A ) Relative ALP activity of hMSCs after 3, 7, and 14 days of co-culture with different samples (* P <0.05, compared to P0 at the same time; # P <0.05, compared to other scaffolds at the same time). ( B ) Images of positive ALP staining. The hMSCs were stained after being cultured with the four scaffolds respectively for 14 days. P2, P4, or P8 represents the PLGA scaffold coated by MBG precursor solution for 2, 4, or 8 times, respectively. P0 represents the unmodified PLGA scaffold. Abbreviations: hMSCs, human mesenchymal stem cells; ALP, alkaline phosphatase; MBG, mesoporous bioactive glass; PLGA, poly(lactic-co-glycolic acid).

Article Snippet: Human mesenchymal stem cells (hMSCs) (ScienCell Research Laboratories, San Diego, CA, USA) were cultured in Minimum Essential Medium Eagle-alpha modification (α-MEM) culture medium supplemented with 20% fetal bovine serum (FBS), 1% penicillin (100 U/mL), and streptomycin sulphate (100 μg/mL) (GibcoBRL, Grand Island, NY, USA).

Techniques: Activity Assay, Staining, Co-Culture Assay, Cell Culture

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A Quantification of Annexin V + cells in Jurkat T lymphoma cells treated with increasing concentrations of anti-FAS antibody (aFAS) for 24 h ( n = 3) and representative Annexin V/PI staining following stimulation with 1 μg/ml of anti-Fas antibody for 24 h. B Quantification of Annexin V + cells in human BM-MSCs treated with increasing concentrations of anti-FAS antibody for 24 h ( n = 3) and representative Annexin V/PI staining following stimulation with 10 μg/ml of anti-Fas antibody for 24 h. C Representative flow cytometric analysis of FAS expression in one of three human BM-MSCs in comparison to peripheral blood mononuclear cells (PBMC). D Quantification of Annexin V + cells in Jurkat cells treated with increasing concentrations of FcFASL for 24 h ( n = 3). E – G Quantification of Annexin V + cells in human BM-MSCs ( E ), mouse BM-MSCs ( F ), and primary MEFs and SV40-immortalised MEFs ( G ) treated with increasing concentrations of FcFASL for 24 h with or without pre-treatment with 50 μM zVAD-FMK for 30 min ( n = 3). H Quantification of Annexin V + cells in human BM-MSCs treated with 10 μg/ml anti-FAS antibody for 24 h in the presence or absence of 500 nM SMAC mimetic (Compound A) with or without pre-treatment with 50 μM zVAD-FMK for 30 min ( n = 3). I Representative Annexin V/PI staining in human BM-MSCs treated with 100 ng/ml TNF for 24 h, and quantification of Annexin V + cells in human BM-MSCs treated with increasing concentrations of TNF ( n = 3). J Quantification of Annexin V + cells in human BM-MSCs (left panel) and mouse BMDMs (right panel) treated with 100 ng/ml TNF, or 25 μg/ml poly(I:C), or 25 μg/ml LPS for 24 h in the presence or absence of 500 nM SMAC mimetic, with or without pre-treatment with the pan-caspase inhibitors Q-VD-OPh or zVAD-FMK for 30 min ( n = 3). K Quantification of Annexin V + cells in human BM-MSCs treated with 100 ng/ml TNF, or 100 μg/ml poly(I:C), or 50 μg/ml LPS for 24 h in the presence or absence of 500 nM SMAC mimetic with or without pre-treatment with increasing concentrations of Q-VD-OPh or zVAD-FMK for 30 min ( n = 3). Data expressed as the mean ± S.E.M. and representative of at least two independent experiments, p values by one-way ANOVA with Tukey’s post hoc test.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Staining, Expressing, Comparison

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A , B Quantification of Annexin V + cells in Jurkat cells ( A ) and human BM-MSCs ( B ) treated with increasing concentrations of the BH3 mimetic drugs ABT199 (BCL-2 inhibitor, iBCL2), A1331852 (BCL-XL inhibitor, iBCLxL) for 3 h. C Representative Annexin V/PI staining in human BM-MSCs treated with increasing concentrations of BH3 mimetic drugs, and BAK/BAX-deficient (BKX) MSCs treated with 1.25 μM BH3 mimetic drugs for 3 h. D Quantification of Annexin V + cells in human MSCs ( D ) and mouse MSCs ( E ) treated with increasing concentrations of BH3 mimetic drugs for 2 h ( n = 3). F , G Quantification of Annexin V + cells at various time points following treatment of human MSCs with 1.25 μM BH3 mimetic drugs ( F ) and mouse MSCs, MEFs and BAK/BAX deficient MEFs treated with 10 μM BH3 mimetic drugs ( G ) ( n = 3). H Quantification of Annexin V + cells in human MSCs treated with increasing concentrations of various BH3 mimetic drugs combinations for 24 h ( n = 3). I Quantification of Annexin V + cells in mouse MSCs treated with various BH3 mimetic drugs combinations at 10 μM for 24 h ( n = 3). Data expressed as the mean ± S.E.M. and representative of at least two independent experiments.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Staining

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A Quantification of live cells (Annexin V − ) in human AD-MSCs, UC-MSCs, and BM-MSCs treated with increasing concentrations of BH3 mimetic drugs for 2 h ( n = 3 donors per tissue type). B Relative expression level of the anti-apoptotic genes BCL-XL , BCL-2 , and MCL-1 in cultured AD-MSCs, UC-MSCs, and BM-MSCs ( n = 3 donors per tissue type). Data expressed as the mean ± S.E.M. pooled from two independent experiments, p values by one-way ANOVA with Tukey’s post hoc test.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Expressing, Cell Culture

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A , B Representative Annexin V/PI staining in unprimed BM-MSCs and BM-MSCs primed with single (TNF or IFN-γ) or dual (TNF and IFN-γ) cytokines at the indicated concentrations for 24 h prior to treatment with vehicle control (DMSO) ( A ) or 1.25 μM BH3 mimetic drugs ( B ) for 2.5 h. C Representative Annexin V/PI staining of two additional BM-MSC donors primed with 10 ng/ml TNF and 100 ng/ml IFN-γ for 24 h prior to treatment with BH3 mimetic drugs for 2.5 h. D Quantification of the proportion of live Annexin V − PI − cells (left panel), early Annexin V + PI − (middle panel) and late Annexin V + PI + apoptotic cells (right panel) in unprimed and primed BM-MSCs from three donors treated with increasing concentrations of BH3 mimetic drugs for 2.5 h ( n = 3). E Representative Annexin V/PI staining in unprimed and primed BM-MSCs treated with 0.125 μM BH3 mimetic drugs for 2.5 h. F Quantification of live (Annexin V − PI − ), early apoptotic (Annexin V + PI - ) and late apoptotic (Annexin V + PI + ) cells from three BM-MSC donors treated with 0.125 μM BH3 mimetic drugs (as shown in E ) for 2.5 h ( n = 3). G Representative Annexin V/PI staining in unprimed and primed MSCs treated with 1.25 μM BH3 mimetic drugs for 30 min. H Representative Annexin V/TO-PRO-3 staining and gating of Annexin V + TO-PRO-3 hi late apoptotic cells in unprimed and primed BM-MSCs treated with BH3 mimetic drugs for 30 min. I , J Representative histograms showing the proportion of TO-PRO-3 int cells after exclusion of Annexin V + TO-PRO-3 hi late apoptotic (as shown in H ) in unprimed and primed BM-MSCs treated with BH3 mimetic drugs (blue histograms) or vehicle (grey histograms) for 30 min. Data expressed as the mean ± S.E.M. and representative of two independent experiments, p values by two-way ANOVA with Dunnett’s multiple comparison test.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Staining, Control, Comparison

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A Live cell imaging of parental MSCs (top panels; Video ) and apoptosis-deficient BKX-MSCs (bottom panels; Video ) following apoptosis induction with BH3 mimetic drugs. B Live cell imaging of untreated human bone marrow MSCs (top panels; Video ) and BH3 mimetic drug-treated MSCs (bottom panels; Video ) stained with Annexin V, showing formation of apoptotic bodies (arrows). C Representative Annexin V staining (left panel) and quantification of the proportion of apoptotic bodies (right panel) in human MSCs treated with BH3 mimetic drugs ( n = 3). Data are expressed as the mean ± S.E.M and representative of three independent experiments. D Schematic for detection of MSCs and apoptotic bodies within the lungs at various time points after intravenous injection into mice. E Representative staining for CTV and CD45 to detect MSCs in digested lung tissue harvested 10 min post intravenous MSC injection F Representative staining for active caspase 3 within the CTV + cell population, used to identify apoptotic MSCs and apoptotic bodies within digested lung tissue following intravenous injection of CTV-labelled parental MSCs (top panel) or BKX-MSCs (bottom panel). G Quantification of apoptotic bodies detected in the lungs of mice (as shown in E ). Data represent the mean ± S.E.M. of n = 3 mice, p values by one-way ANOVA with Tukey’s post hoc test. Panel D was created with BioRender.com.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Live Cell Imaging, Staining, Injection

Journal: Cell Death Discovery

Article Title: Proinflammatory cytokines sensitise mesenchymal stromal cells to apoptosis

doi: 10.1038/s41420-025-02412-0

Figure Lengend Snippet: A Schematic of how the survival of unprimed and primed MSCs was analysed within mouse lung tissue. B Representative staining for CTV and hCD73 to detect MSCs in digested lung tissue harvested 30 min post intravenous MSC injection. C Gating strategy used to identify live MSCs, apoptotic MSCs and apoptotic bodies, based on pooled samples of viable MSCs and BH3-mimetic drug treated MSCs stained with FLICA to detect active caspase 3/7. D Representative FLICA staining within the CTV + cell population used to detect live MSCs, apoptotic MSCs and apoptotic bodies in digested lung tissue. E Quantification of the number of live MSCs, apoptotic MSCs and apoptotic bodies within the lungs (as shown in D ). F Quantification of the proportion of CD45 − (left panel) and CD45 + cells (right panel) within the CTV + FLICA + apoptotic MSC gate. G , H Detection of human CD73 + MSCs within ex vivo cultured lung cells. Digested lung cells from untreated mice, or mice that received intravenous unprimed MSCs or primed MSCs were cultured for six days and the number of human MSCs was quantified. G Representative staining of human CD73 + MSCs within the CD45 − population of cultured lung cells. H Quantification of the number (left panel) and proportion (right panel) of human CD73 + MSCs in cultured lung cells six days after plating. Data represent the mean ± S.E.M. of n = 3 mice, unpaired T -test; ** p ≤ 0.01. Panel A was created with BioRender.com.

Article Snippet: Human adipose-derived MSCs were either purchased from ScienCell or isolated from subcutaneous adipose tissue obtained from outpatient liposuction procedures (Monash human ethics approval #2007/1798; performed with informed patient consent).

Techniques: Staining, Injection, Ex Vivo, Cell Culture