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34 protocols using sodium azide

1

Quantifying PA14 Colonization in Worms

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The quantification procedure of intestinal PA14 colony forming units (CFU) was modified from a previous study (39 (link)). Briefly, after exposure to P. aeruginosa PA14 for 24 hours, ten worms were transferred onto a fresh 3.5 cm NGM plate with M9 solution containing 25 mM sodium azide (Amresco, 0639) to paralyze the worms. Worms were then washed once by M9 solution containing 1 mg/ml ampicillin and 1 mg/ml gentamicin (Solarbio, G8170, China) and incubated for 0.5 h to kill bacteria attached to the surface of the animals on the plate. After worms were lysed with a motorized pestle, serial dilutions of the lysates (10-1, 10-2, 10-3, 10-4) were plated onto Luria-Bertani plates containing 100 g ml-1 rifampicin (Solarbio, R8011) and incubated overnight at 37°C to select for PA14 colony. PA14 colonies were counted to determine CFU per worm. At least three independent replicates were performed for each condition.
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2

Brain and Spleen Tissue Preparation

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At the end of each feeding period (5 or 12 weeks), all mice were terminally overdosed with sodium pentabarbitone (250 mg/kg, LethobarbTM, Tory laboratories, Glendenning, NSW, Australia) and perfused with 30 mL of 0.9% saline followed by 50 mL of cold 4% paraformaldehyde (PFA, Sigma-Aldrich) for ~5 minutes (min). Brain and spleen samples were collected and post fixed with 4% PFA at 4 °C for one week and stored in 0.01 M phosphate buffered saline (PBS, Sigma-Aldrich) solution containing 0.02% sodium azide (Amresco, Solon, OH, USA) at 4 °C for ≤1 month or until sectioned. Spleen weights were measured (n = 3 and 5 from 5- and 12-week studies, respectively) and expressed as a function of body weight (Supplementary Figure S5c). Prior to sectioning, whole brain and spleen were immersed in 30% sucrose for 48 h at RT for cryo-protection followed by embedding in 4% gelatine (Chem-Supply, Gillman, SA, Australia) at −20 °C. Brains (5 weeks: 50 µm and 12 weeks: 40 µm) and spleen (20 µm) were sectioned coronally on a Leica cryostat (Leica, Wetzlar, HE, Germany). Sections were transferred to either 6-well plate (Sakura, Torrance, CA, USA) containing cold (5–6 °C) 0.01 M PBS (free floating) or mounted onto 0.5% gelatine-coated slides (Knittel Glass, Braunschweig, NI, Germany) as described previously [65 (link)].
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3

Quantifying Pseudomonas Infection in Worms

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The worms were exposed to P. aeruginosa PA14 as described above. After infection for 24 h, worms were transferred to M9 solution containing 25 mM sodium azide (Amresco, 0639) to paralyze the worms and stop the pharyngeal pumping. Worms were washed three times with an antibiotic M9 solution containing 1 mg/ml ampicillin and 1 mg/ml gentamicin (Solarbio, G8170, China) followed by 30 min of incubation in the antibiotic solution to kill the bacteria present on the exterior of the worms. After transfer onto the new NGM plates containing 1 mg/ml ampicillin and 1 mg/ml gentamicin for another 30 min to further eliminate the external P. aeruginosa PA14, the worms were lysed with a motorized pestle. Lysates were serially diluted with M9 buffer and plated on Luria-Bertani plates containing 100 μg/ml rifampicin (Solarbio, R8011, China) to select for P. aeruginosa PA14. After overnight incubation at 37 °C, colonies of P. aeruginosa PA14 were counted to determine CFU per worm. Ten worms were examined per treatment, and at least three replicate assays were performed.
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4

Comprehensive Immune Cell Profiling

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When indicated, cells from both experimental groups were recovered by means of peritoneal lavage and maintained in buffer 1 (sterile 1 × PBS supplemented with FBS 10% and 2 mM EDTA, Cytiva, USA). Peritoneal cells were counted and adjusted at 1 × 10 6 cells/ml and transferred into flow cytometry buffer (PBS with 1% FBS and 0.05% sodium azide, Amresco, USA) in order to proceed for staining. Cell samples were incubated 30 min. at 4 °C with the combinations of fluorochrome-conjugated antibodies as follows: suppressive macrophages (PECy7-F480, PE-PDL1, and APC-PDL2), eosinophils (PECy7-F480 and APC-Siglec F), and B regs (APC-CD19, PE-PDL1 and BV421-PDL2). Samples were acquired in Attune® NXT and analyzed with FlowJo V10 software (USA), representative plots gated on singlets, and live cells are shown.
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5

Mass Spectrometry Protein Analysis

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LC-MS grade acetonitrile and water were from J.T. Baker (Philipsburg, NJ). Formic acid, tris (2-carboxyethyl) phosphine (TCEP), and Protein-A/G MagnaBind® beads were from Pierce (Rockford, IL). Iodoacetamide (IAA), BSA, aprotinin, and EDTA were obtained from Sigma-Aldrich (St. Louis, MO). Sodium chloride (NaCl) and sodium fluoride (NaF) were supplied by BDH (West Chester, PA). Protease inhibitors antipain, leupeptin, benzamidine, pepstatin, and sodium azide (NaN3) as well as Triton X-100 were purchased from Amresco (Solon, OH) and PMSF from CalBiochem (Darmstadt, Germany). Sequencing grade Lys-C and trypsin were from Roche (Mannheim, Germany) and Promega (Madison, WI), respectively.
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Immunofluorescent Staining of NK Cells

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For surface fluorescent immunostaining cells were incubated with Abs for 30 min on ice in PBA staining buffer (PBS containing 0.5% BSA (Serva, Heidelberg, Germany) and 0.01% sodium azide (AMRESCO, Inc. (VWR International, LLC), Aurora, CO, USA)) and then washed twice in the same buffer. Some samples were stained with Hoechst 33342 (FluoroPure Grade, Thermo Fisher Scientific, USA) during 45 min on water bath (+37°C). Samples were analyzed in FACSCalibur flow cytometer (BD Biosciences, USA), equipped with 488 and 640 nm lasers. Samples labeled with Hoechst 33342 were analyzed on FACSVantage DiVa machine (BD Biosciences, San Jose, CA, USA) equipped with 405, 488, and 643 nm lasers. From 50,000 to 300,000 events for freshly isolated NK cells and from 5000 to 30,000 events for NK cell fractions and clones in FSC-SSC gate were recorded.
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7

SDS-PAGE Reagent and Equipment

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Dulbecco's modified Eagle medium: Nutrient Mixture F-12 (DMEM/F12) (1:1) was purchased from HyClone (Logan, Utah, USA). Fetal bovine serum was obtained from Sijiqing (Hangzhou, China). Gelatin, acrylamide, N,N'-methylenebisacrylamide, glycine, sodium dodecyl sulfate, Triton TM X-100, ethylenediaminetetraacetic acid, Coomassie Brilliant Blue R-250, and sodium azide were from AMRESCO (Solon, OH, USA). Pre-stained protein markers were purchased from Fermentas Co. (Beijing, China). Other reagents were all manufactured domestically to analytical purity. Vertical electrophoresis tanks and the gel imaging apparatus were from Bio-Rad (Hercules, CA, USA).
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8

Analytical Characterization of HER-2 Protein

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The carrier for the AF4 was prepared from analytical grade sodium chloride (prod. no. 27788.297, VWR), di-sodium phosphate dihydrate (prod. no. 28029.292, VWR), potassium phosphate (prod. no. 26936.293, VWR), potassium chloride (prod. no. 26764.298, VWR) and sodium azide (prod. no. 103692K, VWR). For the aggregation buffer, sodium acetate (prod. no. A13184, Alfa Aesar) was used. Water used for the preparation was purified on an ion-exchange unit (Purelab Ultra, ELGA). Standard proteins myoglobin (prod. no. M1882), ovalbumin (prod. no. A5503), bovine serum albumin (prod. no. A3059), immunoglobulin G (prod. no. 56834) and thyroglobulin (prod. no. T1001) as well as the human serum (prod. no. H4522) were obtained from Sigma-Aldrich.
The trastuzumab was obtained from a Swedish pharmacy (Apoteket AB). Purified HER-2 was acquired in two modified forms from Sino Biological Inc.: His-tagged (prod. no. 10004-H08H) and biotinylated and His-tagged (prod. no. 10004-H08H-B). The molecular weight of the HER-2 protein was 71 kDa, and after reconstitution, the concentration of both stock solutions was 250 μg/mL.
Biotinylated Au sensors, NTA-modified carboxymethyldextran sensors (CMD-NTA) and unmodified carboxymethyldextran sensors (CMD) were provided by BioNavis Ltd.
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9

De-cellularized Breast Tumor Scaffolds

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Patient-derived breast tumors were collected via the clinical pathology diagnostic unit at Sahlgrenska University Hospital. Processing of patient material and data has been approved by the Regional Research Ethics Committee in Gothenburg (DNR: 515-12 and T972-18). The tumors were de-cellularized as described in a previous study by Landberg et al. (2020a) (link). In brief, breast tumors were de-cellularized in a lysis buffer containing 0.1% SDS (Sigma-Aldrich), 0.02% sodium azide (VWR), 5 mM 2H2O-Na2-EDTA (Sigma-Aldrich), and 0.4 mM phenylmethanesulfonyl fluoride (Sigma-Aldrich). Scaffolds were washed in a lysis buffer lacking SDS followed by washing in distilled water and PDS (Medicago). Washed scaffolds were sterilized in 0.1% peracetic acid (Sigma-Aldrich), washed in PBS supplemented with 1% Antibiotic–Antimycotic (ThermoFischer Scientific), and stored at 4°C in PBS (Medicago) containing 0.02% Na-azide (VWR) and 5 mM 2H2O-Na2-EDTA (Sigma-Aldrich). Prior to use, scaffolds were cut to about 3 × 3 × 3 mm size.
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10

Perfusion and Tissue Fixation Protocol

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All tissues were dissected 4h after the last post-drug treatment, passing the KXA half-life of 2–3 h (Zhang et al., 2018 ). For histological analysis, animals were quickly anesthetized with isoflurane (Zoetis, Cat#6089373) and secured to the perfusion plate. The chest was open to expose the heart. The left ventricle was cannulated and the inferior vena cava cut. The animals were initially perfused with 20 ml of phosphate-buffered saline (PBS) with heparin (100 mg/l, Sigma, Cat#H0878), followed by 20 ml of 4% (w/v) paraformaldehyde (PFA, Sigma, Cat#P6148) in PBS using a peristaltic pump (Behr, Cat#PLP 380, speed: 25 rpm). The animals were decapitated, the retina and brain explanted and post-fixed in 4% (w/v) PFA/PBS for 30 minutes and overnight (16h), respectively. Then the tissues were washed in PBS and stored at 4°C with 0.025% (w/v) sodium azide (VWR, Cat#786–299). For cryoprotection, the tissue was transferred to 30% (w/v) sucrose (Sigma, Cat#84097) in PBS and incubated overnight at 4°C. To increase antibody permeability, the brain slices were frozen over dry-ice and thawed at room temperature for three cycles. Then, the brain was sliced in 100 μm coronal slices on a vibratome (Leica VT 1200S), if not otherwise indicated. For parasagittal sections, the brain was divided along the midline and the same vibratome settings were used.
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