type i collagen fibers  (Thermo Fisher)

Journal: International Journal of Biological Sciences

Article Title: Interaction between m6A and YAP1 mechanotransduction pathways is essential for mechanical memory and matrix remodeling in pancreatic cancer

doi: 10.7150/ijbs.125330

Figure Lengend Snippet: CD166 promotes PDAC tumor stiffness through LOXL2. (A, C) Results of elastography to test the tumor stiffness in the in situ PDAC tumor model. (B, D) Results of Masson's trichrome staining to detect the degree of fibrosis of the in situ tumor model of PDAC. (E-F) Results of the matrix cross-linking experiment of BxPC-3 PDAC cells after knocking down CD166 (E) and LOXL2 (F). (G-H) An electronic universal testing machine is used to measure the matrix stiffness of collagen fibers after 3D culture. (I-J) Morphological changes in the type I collagen fiber matrix observed under an electron microscope after knocking down CD166 (I) and LOXL2 (J). (K-L) Tumor size in the in situ tumor model mice. (M-N) Tumor weight in the in situ tumor model mice.

Article Snippet: Ten million pancreatic cancer cells from culture dishes were digested and resuspended in 500 μL type I collagen fibers (Thermo Fisher, USA).

Techniques: In Situ, Staining, Microscopy

Journal: PLoS ONE

Article Title: Structural and Functional Characterization of Mature Forms of Metalloprotease E495 from Arctic Sea-Ice Bacterium Pseudoalteromonas sp. SM495

doi: 10.1371/journal.pone.0035442

Figure Lengend Snippet: The substrate specificities of E495-M towards proteins and synthetic peptides.

Article Snippet: Insoluble type I collagen fiber (bovine Achilles tendon) was purchased from Worthington Biochemical Co. (USA), alpha casein, azoalbumin, gamma globulin and elastin (bovine neck ligament) from Sigma (USA), gelatin from Boston Biomedical Inc (USA), skim milk from Becton Dickinson Company (USA) and synthetic substrates, FA-Gly-Phe-NH 2 (FAGFA), FA-Gly-Leu-NH 2 (FAGLA) and FA-Gly-Val-NH 2 (FAGVA) from Bachem A (Bubendorf, Switzerland).

Techniques:

Journal: Nature Communications

Article Title: Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis

doi: 10.1038/s41467-022-28264-1

Figure Lengend Snippet: a RMSD of the backbone atoms of the unbound-CM and unbound-CM: THP complex structures. b Analysis of the conformational change of the first principal component in the unbound-CM MDS. c RMSF of the CM residues in the MDS of the unbound-CM and unbound-CM: THP structures. d Radius of gyration ( R g ) of the unbound-CM and unbound-CM: THP structures over simulated time. e The most populated cluster during the MDS of the unbound-CM: THP binary complex. The catalytic Glu478 (magenta) and double-Gly motif (orange) are labeled. The THP is indicated as surface and colored in yellow. f The activities of VhaC (WT) and its mutants towards type I collagen fibers, [(POG) 10 ] 3 , and Pz peptide. The specific activities of VhaC towards collagen fibers, [(POG) 10 ] 3 and Pz peptide were taken as 100%. Data shown are mean ± SD ( n = 3 independent experiments). For comparison of the statistical differences between two groups, a two-tailed t -test was used in statistical analysis. * p < 0.01. ** p < 0.001. ns, no significant difference ( P ≥ 0.01). # The significance was not compared due to the activity of the enzyme was undetectable. The p -values in all cases were compared with the corresponding wild type, and provided in the source data. g CD spectra of VhaC (WT) and its mutants. The data shown are representatives of triplicate experiments. Source data are provided as a Source Data file.

Article Snippet: Type I collagen fibers from bovine achilles tendon were purchased from Worthington Biochemical Co., (USA).

Techniques: Labeling, Two Tailed Test, Activity Assay

Journal: Nature Communications

Article Title: Structure of Vibrio collagenase VhaC provides insight into the mechanism of bacterial collagenolysis

doi: 10.1038/s41467-022-28264-1

Figure Lengend Snippet: a The activities of VhaC, ΔPKD, and ΔPPC towards collagen fibers, [(POG) 10 ] 3 , and Pz peptide. The specific activities of VhaC (WT) towards type I collagen fibers, [(POG) 10 ] 3 , and Pz peptide were taken as 100%. b Fluorescence analysis of the collagen-binding ability of EGFP, EGFP-PKD, and EGFP-PPC. c The collagen-binding ability of EGFP-PPC (WT) and its mutants. d Surface representation of the interface with collagen in the homology-modeled PPC domain. Residues involved in interacting with collagen are shown as cyan sticks. e CD spectra of EGFP-PPC (WT) and its mutants. The data shown are representatives of triplicate experiments. Data shown in figures a–c are means ± SD ( n = 3 independent experiments). For comparison of the statistical differences between two groups, a two-tailed t -test was used in statistical analysis. * p < 0.01. ** p < 0.001. ns, no significant difference ( P ≥ 0.01). The p -values in all cases were compared with the corresponding wild type, and provided in the source data. Source data are provided as a Source Data file.

Article Snippet: Type I collagen fibers from bovine achilles tendon were purchased from Worthington Biochemical Co., (USA).

Techniques: Fluorescence, Binding Assay, Two Tailed Test