Journal: Retrovirology

Article Title: Extracellular vesicles from HTLV-1 infected cells modulate target cells and viral spread

doi: 10.1186/s12977-021-00550-8

Figure Lengend Snippet: Functional Effects of HTLV-1 EVs on Angiogenesis and Inflammation. a An angiogenesis assay in technical and biological triplicate was used to determine the effect of distinct HTLV-1 EVs (2 k, 10 k, and 100 k) on tubular formation in a co-culture of mesenchymal stem cells (MSCs) and aortic endothelial cells (AEC). EV-treated cells (1:2000 recipient cell to EV ratio). Positive control cells received complete, undiluted medium. Additional dose of EV treatment was given to the cells at day 4. Representative images were taken at days 3 and 6 showing tubular formation in response to the indicated treatment. b The image processing software WIMASIS was used to calculate the percentage of area covered by tubules (n = 3) on day 3 and day 6. c RT-qPCR results showing env RNA copy numbers of mesenchymal stem cells treated with CEM EVs (control) and different populations of HTLV-1 EVs: 2 k (left panel), 10 k (middle panel), and 100 k (right panel). A set of dashed black vertical lines (---) were used to indicate baseline env RNA copy numbers. A set of dashed red vertical lines ( ) were used to indicate the levels of starting material, suggestive of the minimum env RNA copy numbers necessary for EVs to increase vial spread in MSc. d Western blot analysis for core histones (H3, H2A, H2B, and H4), linker histone (H1) and actin in HUT102 EVs (2 k, 10 k, and 100 k). e GAPDH DNA levels (representative of nucleosomes) in 2 k, 10 k, and 100 k HUT102 EVs treated with proteinase K and DNase/RNase were evaluated by was quantitated by q-PCR. A two-tailed student t-test was used to evaluate statistical significance with “**” for p-values ≤ 0.01, indicating the level of significance relative to untreated (Control) samples

Article Snippet: Bone marrow derived Mesenchymal Stem Cells (MSCs) were cultured in Mesenchymal Stem Cell Basal Medium (ATCC PCS-500–030TM) supplemented with Mesenchymal Stem Cell Growth Kit for Bone Marrow-derived MSCs (ATCC PCS-500-041TM).

Techniques: Functional Assay, Angiogenesis Assay, Co-Culture Assay, Positive Control, Software, Quantitative RT-PCR, Control, Western Blot, Two Tailed Test

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

Journal: Experimental cell research

Article Title: Tumor stroma interaction is mediated by monocarboxylate metabolism

doi: 10.1016/j.yexcr.2017.01.013

Figure Lengend Snippet: Glycolytic flux and lactate metabolism. (A) The extracellular acidification rate (ECAR; mean±SD) of MDA-MB-231 cells and CAFs, measured by Seahorse analyzer, reveals that MDA-MB-231 cells are more glycolytic than CAFs. The extracellular acidification rate ECAR measures proton excretion (representing cellular glycolysis) over time in units mpH/min where 1 mpH = 4.3 pmole excreted H+. (B) Extracellular glucose consumption and lactate production of MDA-MB-231 cells and stromal cells confirm the higher glycolytic activity of MDA-MB-231 cells compared to CAFs observed by Seahorse Analyzer analysis. Data are displayed as mean±SD (n = 3). (C) The glucose uptake is significantly higher in MDA-MB-231 cells (MDAs) than in MSCs or CAFs, in good agreement with the higher aerobic glycolysis observed in the cancer cells. Data are displayed as mean±SD (n = 4). (D) CAFs take up and metabolize lactate as well as secrete lactate oxidation metabolites, as shown by 13C MR spectroscopy on cell extracts and CCM. Signal assignments are: α-KG – α-ketoglutarate, Glu – glutamate; Ala – alanine; Lac – lactate; Pyr – pyruvate; α-Glc & β-Glc – α-glucose and β-glucose; “-C” followed by number – position of 13C labeling as a result of metabolic conversion of exogenous 10 mM 3-13C-L-lactate. ** p<0.005, *** p<0.0005 by two-tailed, unpaired, unequal variance Student’s T-test; Abbreviations: MDAs – MDA-MB-231 cells; MSCs: human mesenchymal stem cells; CAFs: cancer-associated fibroblasts; CCM – CAF-conditioned medium;

Article Snippet: Bone marrow-derived mesenchymal stem cells (MSCs) were purchased from Lonza Walkersville, Inc. (Walkersville, MD; Lonza Group Ltd.).

Techniques: Activity Assay, Spectroscopy, Labeling, Two Tailed Test

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