Journal: bioRxiv

Article Title: Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin

doi: 10.1101/484568

Figure Lengend Snippet: A schematic workflow of nucleolar isolation. Details that differ between the crosslinked and non-crosslinked versions of the preparation are illustrated in . Comparison of NADs to heterochromatin features, and analysis of NAD-seq by multiple bioinformatic packages, including NADfinder . All data shown are from MEF cells. In this panel, the strongly nucleolar-associated chromosome 19 is shown in its entirety. Tracks shown from the top are DNA Replication timing data (early replicating regions have positive values) and LADs (red, ). Below those are raw sequence data from crosslinked cells (blue, experiment #26): read counts for total genomic DNA (Genomic), nucleolar-associated DNA (Nucleolar), and the Nucleolar/Genomic ratio. Next are shown comparisons of peaks called by the bioinformatic packages MACS (broad peaks setting), EDD (50K bins), Hidden Domains (50K bins), and normr (50K bins, v1<0.01, q<10e-03). At the bottom are peaks called by NADfinder (default cutoff q<0.05). All software tested except NADfinder called almost the entire chromosome as peaks. NADs called by NADfinder generally correlate with LADs and late replication timing. As in , showing chromosome 5. Note the gradual decrease in the ratio going from left to right (away from the centromere on the left of this acrocentric chromosome). Unlike MACs and EDD, NADfinder was able to call peaks on regions distal from the centromere.

Article Snippet: An additional plate grown in parallel was reserved for total genomic DNA extraction (Quick-DNA Universal Kit (Zymo Research, CA)).

Techniques: Isolation, Sequencing, Software

Journal: bioRxiv

Article Title: Two Contrasting Classes of Nucleolus-Associated Domains in Mouse Fibroblast Heterochromatin

doi: 10.1101/484568

Figure Lengend Snippet: Schematic representation of crosslinked and non-crosslinked methods used for isolation of nucleoli. The abbreviations of the fractions analyzed by immunoblotting in panel D are indicated. Phase microscopy images of nucleoli purified via crosslinked (experiment #24, see Supplemental Table S1) and non-crosslinked (experiment #29) methods (20x magnification, scale bar 10 μm). qPCR analyses of rDNA enrichment in purified nucleoli compared to genomic DNA. We observed 30-50-fold rDNA enrichment in purified non-crosslinked nucleoli (experiment #33), depending on the primer set used. An 8-13-fold enrichment was observed in crosslinked samples (mean values for experiments #24, 26, 28). Immunoblot analyses of crosslinked and non-crosslinked preparations. Fibrillarin was used as a nucleolar (nus) marker. Nuclear periphery proteins (porin Nup62 and LaminA/C) were present in total (tot) and crude nuclear (nuc, S1) extracts, but depleted from nucleolar (nus) fractions. Cytoskeletal protein actin was enriched in total and crude cytosolic (cyt, S1) fractions, but not in nucleoplasmic (np) or nucleolar (nus) fractions. Analysis of RNAs from fractions obtained during a non-crosslinked preparation. The nucleolar-specific small RNA U3 as well as the ribosomal 5S species are illustrated.

Article Snippet: An additional plate grown in parallel was reserved for total genomic DNA extraction (Quick-DNA Universal Kit (Zymo Research, CA)).

Techniques: Isolation, Western Blot, Microscopy, Purification, Marker

Journal: Canadian Respiratory Journal

Article Title: Extracorporeal Shock Waves Increase Markers of Cellular Proliferation in Bronchial Epithelium and in Primary Bronchial Fibroblasts of COPD Patients

doi: 10.1155/2020/1524716

Figure Lengend Snippet: List of ELISA tests, cell proliferation, and protein extraction kits used. For ELISA tests, dilution of the supernatants or cell lysate samples used and detection limits are also reported.

Article Snippet: c-Kit or SCFR (CD117) , Cloud-Clone Corp. , SEA121 Hu , 1 : 5 (PBS) , 0.61 ng/mL (1.56–100 ng/mL).

Techniques: Enzyme-linked Immunosorbent Assay, Protein Extraction

Journal: Canadian Respiratory Journal

Article Title: Extracorporeal Shock Waves Increase Markers of Cellular Proliferation in Bronchial Epithelium and in Primary Bronchial Fibroblasts of COPD Patients

doi: 10.1155/2020/1524716

Figure Lengend Snippet: C-Kit (CD117) mRNA (a, b, c) and protein (d, e, f) expression after ESW treatment in primary bronchial fibroblasts of COPD patients (a, d), primary bronchial fibroblasts of control smokers (b, e), and bronchial epithelial cells (c, f). In bronchial epithelium (16HBE) c-Kit increased at mRNA (c) and protein (f) levels. In primary bronchial fibroblasts of COPD patients, c-Kit increased at protein level (d). T -test was used for comparative purposes, and p values are reported in the graphs.

Article Snippet: c-Kit or SCFR (CD117) , Cloud-Clone Corp. , SEA121 Hu , 1 : 5 (PBS) , 0.61 ng/mL (1.56–100 ng/mL).

Techniques: Expressing

Journal: Canadian Respiratory Journal

Article Title: Extracorporeal Shock Waves Increase Markers of Cellular Proliferation in Bronchial Epithelium and in Primary Bronchial Fibroblasts of COPD Patients

doi: 10.1155/2020/1524716

Figure Lengend Snippet: Photomicrographs showing thyroid transcription factor-1 (TTF-1) expression (panels a, b), c-Kit (CD117) (c, d), and proliferating cell nuclear antigen (PCNA) (e, f) in the peripheral lung tissue of a representative patient with chronic obstructive pulmonary disease (COPD). Arrows indicate positively stained cells mainly located in the alveolar septa. Bars = 50 microns.

Article Snippet: c-Kit or SCFR (CD117) , Cloud-Clone Corp. , SEA121 Hu , 1 : 5 (PBS) , 0.61 ng/mL (1.56–100 ng/mL).

Techniques: Expressing, Staining

Journal: Canadian Respiratory Journal

Article Title: Extracorporeal Shock Waves Increase Markers of Cellular Proliferation in Bronchial Epithelium and in Primary Bronchial Fibroblasts of COPD Patients

doi: 10.1155/2020/1524716

Figure Lengend Snippet: Photomicrographs showing alveolar type II epithelial cells (TTF-1+ cells, red color) coexpressing c-Kit (CD117) (brown color) (a, b) and PCNA (brown color) (c, d) in the peripheral lung tissue of a representative patient with COPD. Positive double-stained cells can be recognized in the alveolar septa, even though their presence was only rarely observed. Arrows indicate positively stained cells located in the alveolar septa. Bars = 50 microns.

Article Snippet: c-Kit or SCFR (CD117) , Cloud-Clone Corp. , SEA121 Hu , 1 : 5 (PBS) , 0.61 ng/mL (1.56–100 ng/mL).

Techniques: Staining