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9 protocols using silicon wafer

1

Antimicrobial Assessment of Biopolymer Films

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Poly (ethylene glycol) (PEG, (Mw = 400 g/mol), chitosan (Mw = 60,000 g/mol), silicon wafers, agar, Müller–Hinton lysogeny broth, glycerol and acetic acid were all obtained from Sigma-Aldrich Chemical Company (St. Quentin Fallavier, France) and used as received. Alginate (Mw = 100,000 g/mol) was donated by FMC Chemical International AG (Dublin, Ireland) and used as received. Cellulose nanocrystals (L = 100 nm, d = 5 nm) were kindly provided by CelluForce (Montréal, Canada). Both fresh and archaeological waterlogged oak wood (Quercus robur) used in this work was obtained from the Mary Rose Museum, for dimensions see electronic supplementary information (Appendix A). Non-pathogenic Escherichia coli (E. coli, DSM 5451-0599-001) and Bacillus subtilis (B. subtilis, DSM-1970-0110-001) were purchased from the German Collection of Microorganisms and Cell Cultures (DSMZ) GmbH (Braunschweig, Germany). Liquid nitrogen for cryogenic freezing was obtained from Kraiss & Friz e.K., (Remshalden, Germany). Water used in all experiments was obtained from an in-house water deionisation system. Preparation of films for initial microscopy studies and treatment of the wood samples is detailed in Appendix A.1 and Appendix A.2. Protocols for the biological tests are given in Appendix A.3.
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2

TEM and SEM Imaging of Nanoparticle Dispersions

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TEM images were obtained using
a TEM Zeiss CEM 902 (Carl Zeiss AG) with an accelerating voltage of
80 kV. SEM images were obtained using a SEM Zeiss 1530 (Carl Zeiss
AG) equipped with a field-emission cathode with an operating voltage
of 3 kV. Samples were prepared by spin-coating (2000 rpm, 30 s) of
the NP dispersions on silicon wafers (Sigma-Aldrich), cleaned with
Milli-Q water before use, and mounted on SEM aluminum pin stubs (Plano
GmbH).
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3

Culturing Primary Cells with Precise Conditions

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Silicon wafers (2 inch diameter × 0.5 mm thickness) were purchased from Sigma-Aldrich. TGF-β1 (lyophilized) was purchased from Novoprotein. Culture buffers and RPMI media were purchased from Cellgro and Gibco, respectively. Complete RPMI medium was supplemented with 10% fetal bovine serum (HyClone from Thermo Scientific), 330 mg/L of L-glutamine, 96 U/mL of streptomycin, and 22 mL/L of 1 M HEPES buffer. All other reagents, unless otherwise specified, were purchased from Sigma-Aldrich.
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4

Cleaning of Silicon Wafers and Glass Slides

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Silicon wafers (size: 3 inch × 0.387 mm; roughness: 1 nm) (Sigma-Aldrich) and glass slides (size: 76 mm × 26 mm × 1 mm; roughness: <0.15 μm) (MiniMed) were cleaned sequentially with detergent, pure water, acetone, and isopropanol in an ultrasound bath for 15 min. Then, the slides were dried in a flow of nitrogen.
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5

Fabrication of Monolayer PS Templates

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Mono-layer PS templates were prepared following previously described procedure.27,34,35 (link) Silicon wafers (Sigma-Aldrich) were cut into square (∼1.5 × 1.5 cm2) and rectangular (∼1 × 3 cm2) pieces, and sonicated with ethanol. After washing several times with Milli-Q water (Millipore, resistivity of 18.2 MΩ cm−1 at 25 °C) and drying at room temperature, the Silicon wafers were treated with UV/Ozone for 20 minutes to improve wafer hydrophilicity (UV/Ozone ProCleaner™ Plus, BioForce Nanosciences, Inc.). A Petri dish was filled with Milli-Q water, and the PS particle suspension (100 μl, 10 wt%, Bangs Labs) with diameters 280 nm, 210 nm or 99 nm was mixed with an equal amount of ethanol. This mixture was discharged slowly over the rectangular silicon wafer, which was placed in a Petri dish at a sloped plane to the Milli-Q water surface using a micropipette, and the rectangular wafer was then slowly submerged in the water. A sodium dodecyl sulphate (SDS) solution (2%, ∼10 μl) was added to the Petri dish in order to acquire hexagonal close-packed particles. The PS monolayers on the water layer were then lifted off by a square silicon wafer, and dried at room temperature.
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6

Fabrication of PDMS Microchannels via Laser Ablation

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Polydimethylsiloxane (PDMS) was obtained by mixing the elastomer base with the curing agent (SYLGARD® 184 silicone elastomer kit, Dow Corning) in a 1:10 weight ratio. The mixture was degassed under vacuum to remove trapped bubbles of air and cast on a custom made aluminum circular mold that hosted a silicon wafer (Sigma Aldrich) at the bottom. After casting, the mold was placed in a laboratory oven at 100°C for 45 minutes, to heat cure the degassed polymer mixture. The heat cured PDMS was removed from the mold and a microchannel ablated with a CO2 laser (Universal Laser System, V460, 60W) operated with the software CorelDRAW X419. Printing settings were as follow: vector pen mode, power 10%, speed 10%, PPI 1,000. Three PDMS molds were created, each corresponding to a specific microchannel, a specific thin section and a specific flow experiment. The cross section of each channel was triangular (S3 Fig). A summary of the microchannels’ dimensions measured by optical microscopy is given in S1 Table.
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7

Silk Fabric Degumming and Regeneration

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Natural silk filaments were provided by Hangzhou Qiantang Silk Company Ltd, Zhejiang, China. The filaments were woven to obtain a 1/1 natural silk fabric. Sodium carbonate (Na2CO3) was purchased as a powder from Sinopharm Chemical Reagent Company Ltd, Shanghai, China. The natural silk fabric was degummed 3 times using a 0.05 wt.% Na2CO3 solution at 98°C to obtain the SF fabric. Phosphate-buffered saline (PBS) was purchased from the Solarbio Technology Company Ltd, Beijing, China. Alginate (ALG) was purchased as a powder from Sinopharm Chemical Reagent Company Ltd, Shanghai, China. The RSF solution was derived from Bombyx mori cocoons that were dissolved and dialysed (molecular weight cut off 2000) in distilled water for 48 h. Then, the RSF solution was dialysed against a 20 wt.% poly(ethylene glycol) solution (20000 g/mol) for 30 min. The polyelectrolytes were used as received without further purification and were prepared as 1 g/L solutions. silicon wafers were purchased from Ruicai Technology Company Ltd, Suzhou, China. (3-Aminopropyl) triethoxysilane (APTES) was used to form an amination surface on a silicon wafer purchased from Sigma-Aldrich. The chemical structures of the basic materials used to perform the experiments are shown in Fig 1.
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8

Synthesis and Characterization of Copper(II) Complexes

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Materials in all
synthesis procedures were used without any further purifications.
DA hydrochloride (CAS: 62-31-7, s, >98%), trizma base (CAS: 77-86-1,
s, >99%), hydrochloric acid (CAS: 7647-01-0, l, 25%), copper(II)
sulfate
pentahydrate (CAS: 7758-99-8, s, ≥98.0%), acetic acid (CAS:
64-19-7, l, ≥99%), sodium acetate (CAS: 127-09-3, s, ≥99%),
BA (CAS: 10043-35-3, s, ≥99.5%), sodium hydroxide (CAS: 1310-73-2,
s, ≥98%), and silicon wafer (Si 100, CAS: 7440-21-3, s) from
Sigma-Aldrich and ultrapure deionized water from a Hydrolab Ultra
UV system were used.
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9

Synthesis and Characterization of Zinc Nanoparticles

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Zinc acetate (99% pure), 5,5-Dimethyl-1-pyrroline N-oxide (DMPO), silicon wafer and Quartz plate were purchased from Sigma - Aldrich, 40% Urea, Nutrient Broth, Nutrient agar medium, tri-sodium citrate, hexamine and glutaraldehyde solution supplied by Hi-Media, India was used in this study.
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