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86 protocols using scope a1

1

Ginkgo GbPLATZ Proteins Subcellular Localization

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Plant-mPloc (Chou and Shen, 2010 (link)) was used to predict the subcellular localization for amino acid sequences of the 11 GbPLATZs. The sequence predicted with a nuclear localization was submitted to Identification of Nucleus Signal Peptide from Protein Primary Sequence (INSP; Guo et al., 2020 (link)) for nuclear localization signal recognition. To verify the prediction results, six GbPLATZs expressed during ginkgo seed development were tested by protoplast subcellular localization. The CDS of these genes without termination codons were constructed into the pNC-AMP-GFP-C/N vector (Yan et al., 2020 (link)), to obtain 35S::GFP-GbPLATZ2/4/7/8/9/10 and 35S::GbPLATZ2/4/7/8/9/10-GFP. Transient transformation of ginkgo protoplasts mediated by PEG was based on a method optimized by our laboratory (unpublished data). High-activity protoplasts were extracted by enzymatic hydrolysis from the leaves of ginkgo seedlings. Protoplasts and high-quality plasmids were treated with PEG4000 solution for 15 min, for transformation, and incubated for 14 h before observation. Each transient transformation experiment was repeated at least three times. GFP fluorescence was recorded using a fluorescence microscope (Scope A1 Carl Zeiss, Jena, Germany).
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Quantifying Gastric Cancer Angiogenesis and Mast Cells

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Light microscopy integrated with an image analysis system (AXIO, Scope A1, ZEISS, Gottingen, Germany) was utilized [65 (link)]. In sections of primary tumor tissue, lymph node metastases, adjacent gastric normal tissue, and normal lymph nodes, immunostained areas (hot spots) were selected at 10× magnification. Next, MCDPT (Figure 1A–D, respectively) was assessed counting each single immunostained mast cell clearly separated each to other at 40 × magnification. With special regard to MVD, we considered a microvessel each single immunostained endothelial cell or each immunostained endothelial cell with or without a lumen, clearly separated from adjacent microvessels, tumor cells, and other connective tissue elements (Figure 2A–D, respectively) at 40× magnification. To define the evaluated microscopic fields at 40× magnification (ocular lens 10× and objective lens 40×), the corresponding 0.19 mm2 area for each field was measured by semi-automated modality using the program of the above image analysis system.
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Isolation and Characterization of Lactic Acid Bacteria

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Samples were isolated using two selective media, MRS and M17 (Beijing Land Bridge Technology), under both aerobic and anaerobic conditions at 37 and 30°C for 72 h to obtain as many LAB strains as possible. Isolates were selected and purified according to previously published methods (Medeiros et al., 2016 (link)).
All isolates were verified as LAB using a combination of Gram reaction, catalase activity, and morphological analysis. Gram reactions were visualized using an optical microscope (Scope A1; Carl Zeiss Microscopy) under oil immersion at 100‐fold magnification. Colony morphology was recorded using a colony counter Scan1200 (Interscience International). Cocci, bacilli, or coccobacilli colonies that were gram‐positive with a negative catalase result were included in the LAB group (Abosereh et al., 2016 (link)). Isolates were stored at −20°C in MRS broth supplemented with 20% (v/v) glycerol and only activated prior to testing by two sequential transfers in the same broth used in the experiments.
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4

Multimodal Microscopic Characterization of Materials

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The optical microscope (Scope A1 from ZEISS, SLMPLN50× from Olympus, NA = 0.35) measurements were taken with the solution or the dried fibers on the glass slides.
Scanning electron microscope (SEM) measurements were taken on JEOL JSM6700F or Hitachi S-4800 field-emission scanning electron microscopes. The samples with the gold coating were transferred onto the microscope stage and examined at 10 kV.
The transmission electron microscopy (TEM) images were obtained on a JEOL JEM-1400 transmission electron microscope (120 kV). A drop of the dispersed solution of the samples was dropped onto a TEM grid (a copper grid with a 200 mesh) and then dried for observation. Images were recorded with a Gatan multiscan charge-coupled device (CCD) for the collection and processing of digital micrographs.
Thermogravimetric analysis (TGA) measurements were performed at DSC 822e (Piscataway, NJ, USA) with a scanning speed of 10 °C·min−1 over 50–800 °C under a nitrogen atmosphere.
Fourier transform infrared (FTIR) spectra were carried out on a VERTEX-70/70v FT-IR spectrometer (Bruker Optics, Germany) using a KBr pellet method.
X-ray diffraction (XRD) measurements were completed on a DMAX-2500PC diffractometer with Cu Kα radiation (λ = 0.15418 nm) and a graphite monochromator. Samples were examined within 1–30° in the 2θ mode at a speed of 1° min−1.
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5

Immunofluorescence Localization of Hm3A4-Rap in CHO Cells

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CHO cells expressing Hm3A4-Rap were grown on glass slides for approximately 24 h and then fixed in 4% paraformaldehyde, permeabilized with 0.2% Triton X-100, and blocked in PBS containing 10% calf serum. The cells were then stained with TRITC-conjugated anti-mouse Fab specific IgG antibody (T7782, diluted 1:200; Sigma) and FITC-conjugated goat anti-human IgG Fc antibody (GAHFc FITC) (Invitrogen) for 1 h in the dark. This was followed by incubation with DAPI (Invitrogen) nucleic acid (nuclear) staining for 1 min in the dark. The cells were visualized and imaged using confocal immunofluorescence microscopy (Carl Zeiss Scope.A1, Oberkochen, GER). Non-transfected CHO cells were used as the negative control. The expression of Hm3A4-Rap in CHO cells was detected by immunofluorescence microscopy. The ScFv3A4 fragment was detected using GAM-Fab-TRITC and the Fc fragment was detected using GAH-Fc-FITC [28 (link)].
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6

Immunofluorescence Assay for Mitotic Phenotypes

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MDA-231 or Hs578t cells were plated on eight-well chamber slides (Lab-Tek Products, Illinois, USA) and treated with agents the following day as described. After drug treatment, cells were stained according to immunofluorescence described before [11] (link). Mitotic and nuclear phenotypes of at least 100 cells per condition were assessed. Immunofluorescence images were obtained with a Zeiss Scope.A1.
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7

Quantitative Osteoclast Analysis

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TRAcP-positive cells that contained three or more nuclei were considered osteoclasts and counted. Six representative images per coverslip were captured using a Zeiss Scope A.1 conventional light microscope at 5× magnification to evaluate the number and surface area of osteoclasts per field. For each experimental condition, the total number and cell surface area of osteoclasts were manually counted using ImageJ software.
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8

Immunohistochemical Analysis of TMPRSS11d in Tissues

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Cervical (CR802) and esophageal (ES482) tissue arrays including cancer and normal tissues as well as a universal normal tissue array (UNC241) were obtained from US Biomax, Inc. (Rockville, MD). Tissue arrays were deparaffinized with xylene and hydrated with graded ethanol solutions. Antigen retrieval was performed using citrate buffer, reduced pH, and endogenous peroxidases were quenched by incubating slides in 3% H2O2. The arrays were blocked with 2.5% bovine serum albumin (Sigma) in PBS, and incubated overnight at 4°C with 2 μg/ml rabbit anti human TMPRSS11d (HAT Ab1) (ab127031, Abcam, Cambridge, MA) or rabbit anti human TMPRSS11d (HAT Ab2) (HPA052834, Sigma) in a humidity chamber. All washing steps were performed using PBS. As a negative control, non‐immune rabbit IgG (2 μg/ml) (NeoMarkers, Fremont, CA) was used. Bound antibodies were visualized using biotin‐conjugated anti‐rabbit (Vector Laboratories, Burlingame, CA) secondary antibodies, and a Vectastain ABC kit (Vector Laboratories, Burlingame, CA) or HRP conjugated Polymer Anti‐Rabbit (Dako, Carpinteria, CA). 3,3′‐diaminobenzidine (DAB) was used as the substrate (Sigma) and arrays were counterstained with hematoxylin. All microscopic images were acquired on a Zeiss Scope A.1 using digital imaging.
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9

Immunohistochemical Staining of Tissue Slides

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Tissue slides were deparaffinized with xylene and hydrated with graded ethanol solutions. Antigen retrieval was performed using citrate buffer, pH 6.0 (Bethyl Laboratories, Montgomery, TX) and incubation for 1 h in a 73°C water bath. The slides were blocked with 2% bovine serum albumin in PBS, and immunostained overnight at 4°C. Primary antibodies were rabbit anti-matriptase (Calbiochem/EMD Millipore, San Diego, CA), rabbit anti-c-Met (Leica Microsystems Inc., Buffalo Grove, IL), and mouse anti-E-cadherin (Pharmingen/BD Biosciences, San Jose, CA). As negative controls, non-immune mouse IgG (Sigma, St. Louis, MO) or non-immune rabbit IgG (NeoMarkers, Fremont, CA) were used. Bound antibodies were visualized using biotin-conjugated anti-rabbit or anti-mouse (Vector Laboratories, Burlingame, CA) secondary antibodies and a Vectastain ABC kit (Vector Laboratories). 3,3′-diaminobenzidine (DAB) was used as substrate (Sigma, St. Louis, MO) and arrays were counterstained with hematoxylin. All microscopic images were acquired on a Zeiss Scope A.1 using digital imaging.
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10

Fluorescence Microscopy of S. mansoni Damage

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At the end of each experiment, the parasites were transferred to slides bounded
by small amounts of petroleum jelly to prevent the parasites from spilling out
from the slide. The parasites were placed on the slides with a small amount of
culture medium and then were observed with an optical fluorescence microscope
(Zeiss Axio® Scope A1, Axio Vision LE software) using a rhodamine
filter for resorufin (excitation/maximum emission of resorufin 571/585 nm) and
DAP for Hoechst 33258 (Hoechst 352/455 nm maximum excitation/emission) to
evaluate the damage caused to the excretory system and to the integument of
S. mansoni, respectively, as described by Castro et al.
[19 (link)].
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