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: Frontiers in Cellular Neuroscience

Article Title: Bone Marrow Stromal Cells Alleviate Secondary Damage in the Substantia Nigra After Focal Cerebral Infarction in Rats

doi: 10.3389/fncel.2019.00338

Figure Lengend Snippet: Effects of BMSCs treatment on the number of TH, NeuN, and GFAP positive cells in SN, and DA and its metabolites in striatum at 4 weeks after dMCAO. (A) Representative microphotographs of immunohistochemistry for TH (II,VI,X) , NeuN (III,VII,XI) , and GFAP (IV,VIII,XII) in SN. The pictures on the right are magnified from the square area on the left. Scale bar: I, V, IX, 250 μm; II–IV, VI–VIII, X–XII, 50 μm. (B) Quantitative analyses of TH, NeuN, GFAP-positive cells in the SNc at 1 and 4 weeks after dMCAO. Transplantation of BMSCs increased the numbers of TH + [ F (2, 60) = 31.51, p < 0.01] and NeuN + cells [ F (2, 78) = 17.20, p < 0.01], and decreased the number of GFAP + cells [ F (2, 78) = 1848.10, p < 0.01] in the ipsilateral SNc after dMCAO. Each bar represents the mean ± S.D. * p < 0.05 vs. sham-operated group, # p < 0.05 vs. contralateral groups at the same time point and & p < 0.05 vs. ipsilateral vehicle groups ( n = 6 in each group). (C) The DA (I) , DOPAC (II) , and HVA (III) concentrations in striata at 1 and 4 weeks after dMCAO with or without BMSCs transplantation. Transplantation with BMSCs increased the concentration of DA [ F (2, 8) = 6.33, p < 0.05] in the ipsilateral striatum after dMCAO, maintained the concentration of DOPAC [ F (2, 11) = 0.53, p > 0.05] and HVA [ F (2, 11) = 0.67, p > 0.05] in the ipsilateral striatum after dMCAO. Each bar represents the mean ± SD * p < 0.05 vs. sham-operated group and # p < 0.05 vs. contralateral groups at the same time point and & p < 0.05 vs. ipsilateral vehicle groups ( n = 4 in each group). SN, substantia nigra; SNc, substantia nigra compact part; TH, tyrosine hydroxylase; NeuN, neuron-specific nuclear-binding protein; GFAP, Glial fibrillary acidic protein; Sham, sham-operated; BMSCs, bone marrow stromal cells; DA, dopamine; DOPAC, 3,4-dihydroxyphenylacetic acid; HVA, homovanillic acid; con, contralateral; ip, ipsilateral; w, week; dMCAO, distal middle cerebral artery occlusion.

Article Snippet: Over the past two decades, bone marrow stromal cells (BMSCs) based neurorepair has emerged as a promising therapeutic strategy for ischemic stroke.

Techniques: Immunohistochemistry, Transplantation Assay, Concentration Assay, Binding Assay

Journal: Frontiers in Cellular Neuroscience

Article Title: Bone Marrow Stromal Cells Alleviate Secondary Damage in the Substantia Nigra After Focal Cerebral Infarction in Rats

doi: 10.3389/fncel.2019.00338

Figure Lengend Snippet: Cortico-striatum-nigral tract retrograde tracing with PRV-152. (A) PRV-152 was injected into the ipsilateral SNr. Regions of interest (ROI) of PRV-152 positive cell counting were shown. Dark shaded area represents ischemic region after dMCAO; lighter shaded area represents ROI. (B) Schematic illustration of the fluorescent signal of PRV-152 in sham-operated and dMCAO groups with or without BMSCs transplantation after PRV-152 was injected into the ipsilateral SNr. (C) Representative photographs of fluorescent double staining of PRV-152 (green) and DAPI (blue) in the ipsilateral cortex (I–IV) , striatum (V–VIII) and SNr (IX-XII) at 4 days after PRV-152 injection in sham-operated group. (D) Representative photographs of fluorescent double staining of PRV-152 (green) and DAPI (blue) in the ipsilateral cortex (I–IV) , striatum (V–VIII) , and SNr (IX–XII) at 4 weeks after PRV-152 injection in vehicle group. (E) Representative photographs of fluorescent double staining of PRV-152 (green) and DAPI (blue) in the ipsilateral cortex (I–IV) , striatum (V–VIII) and SNr (IX–XII) at 4 weeks after PRV-152 injection in BMSCs group. Scale bar, 50 μm. (F) Quantitative analyses of PRV-152 + cell number in the ipsilateral cortex, striatum and SNr after dMCAO. Transplantation with BMSCs increased PRV-152 + cells in the ipsilateral cortex [ F (2, 19) = 9.85, p < 0.01], striatum [ F (2, 41) = 10.67, p < 0.01] and SNr [ F (2, 19) = 6.05, p < 0.01] after dMCAO. Each bar represents the mean ± SD * p < 0.05 vs. sham-operated group and # p < 0.05 vs. vehicle group ( n = 7 in each group). SNr, substantia nigra pars reticulata; Cor, cortex; Str, striatum; PRV, pseudorabies virus; Sham, sham-operated; w, week; dMCAO, distal middle cerebral artery occlusion; BMSCs, bone marrow stromal cells; DAPI, 4’, 6- diamidino-2-phenylindole.

Article Snippet: Over the past two decades, bone marrow stromal cells (BMSCs) based neurorepair has emerged as a promising therapeutic strategy for ischemic stroke.

Techniques: Retrograde Tracing, Injection, Cell Counting, Transplantation Assay, Double Staining, Virus

Journal: International Journal of Nanomedicine

Article Title: Drug Delivery to the Bone Microenvironment Mediated by Exosomes: An Axiom or Enigma

doi: 10.2147/IJN.S307843

Figure Lengend Snippet: Patents Related to the Diagnostic and Therapeutic Application of Exosomes Towards Bone Disorders

Article Snippet: Bone marrow-derived mesenchymal stem cells (BM-MSCs) and Adipose-derived stem cells (ASCs) , WO2019139762A1 , Zen-Bio, Inc. (US) , Exosome compositions and use thereof for joint disorders and diseases , Filed on 2018/Status pending.

Techniques: Diagnostic Assay, Biomarker Discovery, Derivative Assay, CRISPR, Isolation, Injection, Clinical Proteomics

Journal: Korean Journal of Neurotrauma

Article Title: Evaluation of Bone Marrow-derived Stem Cells and Adipose-derived Stem Cells Co-cultured on Human Nucleus Pulposus Cells: A Pilot Study

doi: 10.13004/kjnt.2020.16.e36

Figure Lengend Snippet: SA-β-gal: senescence associated-β-gal, NP: nucleus pulposus, NPC: nucleus pulposus cell, MSC: mesenchymal stem cell, ADMSC: adipose-derived mesenchymal stem cell, BDMSC: bone marrow-derived mesenchymal stem cell.

Article Snippet: BDMSC complete culture medium (ATCC ® PCS-500-030) plus one MSC growth kit (ATCC ® PCS-500-041) and ADMSC complete culture medium (ATCC ® PCS-500-030) plus one MSC growth kit (ATCC ® PCS-500-040) were used to cultivate both MSCs; this medium consists of 485 mL Human MSC Basal Medium, 35 mL Human MSC-Qualified FBS, 0.5 mL penicillin/streptomycin-amphotericin and 6 mL L-alanyl-L-glutamine.

Techniques: Derivative Assay