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9 protocols using syringe driven filter

1

Extraction and Formulation of Botanical Ingredients

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Rosa multiflora (stem), Lespedeza bicolor (aerial part), Platycladus orientalis (leaves), Castanea crenata (leaves) and Cornus officinalis (fruit) were purchased from the Gyeongbuk Forest Resource Development Institute, the Republic of Korea. The identity of the plants was confirmed by a taxonomist (Dr. Zi-Eum Im) and voucher specimens were deposited (LVPPM 2001–2005) in our laboratory. The dried and crushed parts of each plant were boiled in 30% ethanol (100 g/Liter). The extracts were filtered with Whatman filter paper Number 1 (GE Healthcare, UK Limited, UK), evaporated to dryness, and freeze-dried. A 5% (w/w) and 10% (w/w) ointments of C2RLP were made using petrolatum (Sigma-Aldrich) as a vehicle. For in vitro experiments on various cell lines, the extract was dissolved in the respective media used to grow the cells and then filtered using a 0.22-μm syringe driven filter (Merck Millipore Ltd., Carrigtwohil, Ireland).
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2

HPLC Analysis of Mimosine in LL Extract

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HPLC analysis was performed following the procedure as previously described [96 (link)] using an Agilent 1200 Series HPLC System (Agilent LabX, Santa Clara, CA, USA) to detect the active compounds in the extract and validate the presence of mimosine. The mobile phases used consisted of 5% acetic acid (A) and 95% acetonitrile (B) run through a reverse phase C18 column (Sigma-Aldrich, USA) (internal diameter: 4.6 mm; height: 250 mm; particle size: 5 mm) with the following elution program: 0–10 min, 70% A isocratic, 10–20 min gradient to 40% A, and 20–30 min 40% A isocratic. The program was set at a 1.0 mL/min flow rate at 30 °C with an injection volume of 20 µL. The analysis was run for 60 min, and the data acquisition was performed at a 367 nm wavelength. The LL extract and mimosine were filtered through a 0.22 µm syringe-driven filter (Merck Millipore, Germany) to avoid the blockage of the column. LL extract alone (1 mg/mL) was first run to analyze the different compound fractions present in the extract. In order to determine the peak that represents mimosine, the standard compound mimosine was used at concentrations of 0.2, 1, and 5 mg/mL, followed by running LL extract (200 µg/mL) spiked with the different concentrations of mimosine.
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3

Polyphenol Preparation and Dilution Protocol

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RCE, a dark green powder under the market name Red clover extract IFL 40 (UPS), was donated by Linnea SA, Lavertezzo Piano, Switzerland. RGSE, a rust-coloured powder sold under market name MegaNatural™-Gold, was donated by Canandaigua Concentrate and Polyphenolics, Divisions of Constellation Brands, Inc, Madera, California, USA. ARE is a dark purple coloured powder, donated by Artemis, International, Inc (Fort Wayne, Indiana, USA). It was processed with water and ethanol as an extract solvent. CUR is an orange-coloured powder, obtained from turmeric by a solvent extraction method (97% natural); it was supplied by Indus Biotech, Pune, Maharashtra, India.
Prior to use, each polyphenol was initially solubilised in DMSO 100 mg/ml (Sigma-Aldrich, Gillingham, UK) and filtered with a 0.22-μm syringe driven filter (Millipore, Watford, Hertfordshire, UK). This stock solution was then serially diluted to 1 mg/ml, in DMSO. This solution was further diluted in complete medium (CM) to attain a final working concentration of 300 μg/ml, reducing the total percentage of DMSO to less than or equal to 1%. Subsequently, concentrations ranging between 1 ng/ml and 250 μg/ml were prepared by diluting the working solution with clear DMEM, for brain tumour and normal brain cells, or with clear RPMI, for the pancreatic cancer cell line.
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4

Lentiviral Transduction of HEK293T Cells

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HEK293T cells were seeded onto 10-cm culture dishes. The cells were transfected one day later by using LipofectamineTM 2000 (invitrogen) with lentiviral transducing vector encoding pLKO or shKDM8 and packaging vectors. After 72 h, virus particles were harvested from the medium and filtered through a 0.45-mm syringe-driven filter (Millipore).
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5

Infecting THP-1 Cells with Toxoplasma and Hammondia

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Prior to infection, THP-1 cells were seeded at 1 x 105 cells/well in 24-well plates in cDMEM. To prepare parasites for the infections, HFFs monolayers containing parasite sporozoites were scraped, syringe-lysed, and pelleted (in some cases, freshly excysted oocysts were used). After resuspending the pellet in cDMEM, the parasite mixture was filtered through a 5 μM syringe-driven filter (Millipore). THP-1 cells were infected with either T. gondii or H. hammondi at multiplicity of infection (MOI) of 4, 2 or 1.6. Three biological replicates were made for each parasite infection. THP-1 cells were also mock-infected with parasite filtered through a 0.22 μM syringe-driven filter (Millipore). These protocols are described in detail in [50 (link)].
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6

Dynamic Light Scattering of IN

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For DLS experiments 500 nM BI/D or 3 µM LEDGF/p75 was added to 200 nM IN in the buffer containing 50 mM HEPES, at pH 7.4, 2 mM DTT, 2 mM MgCl2, and 1 M NaCl (buffer was filtered twice with 0.22 µm syringe driven filter from Millipore). DLS signals were recorded at RT (25 °C) using a Malvern Nano series zetasizer instrument, and particle size distribution was calculated.
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7

Synthesis of Multifunctional Polymer Nanoparticles

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PEG-PCL (10 mg), cholesterol-PEG-folate (1 mg), CPPO (2 mg), PFPV or PFBT (1 mg), TPP (0.05 mg) were homogeneously dissolved in 1 mL of tetrahydrofuran (THF). The mixture was then rapidly injected into 10 mL of Milli-Q water under sonication with a sonicator probe (SCIENTZ - II D). Afterward, the THF in the mixture was evaporated through a nitrogen flow, and the remaining solution was filtered through a 0.22 μm syringe-driven filter (Millipore). Ultimately, the obtained POCL dispersion was concentrated by ultrafiltration and used immediately in the following experiments. Other types of nanoparticles, such as POCL/CCPO-, POCL/PFPV-, POCL/TPP-, or POCL/FA-, were prepared according to the same procedure, except for the addition of CPPO, PFPV, TPP, or cholesterol-PEG-folate.
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8

Lentiviral shRNA Production and Transduction

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For virus production, HEK-293 cells (70–80% confluency) were transfected using X-tremeGENE 9 (Roche Diagnostics Ltd., Burgess Hill, UK) according to manufacturer’s manual with 3 μg pCMV-dR 8.91 (packaging vector, Thermo Fisher) + 0.7 μg pCMV-VSV-G (envelope vector, Thermo Fisher) + 3 μg Lentiviral shRNA vectors (three pLKO1-Puro vectors targeting all Fbln2 variants of the mouse under control of the human U6 promotor (Clones: TRCN0000109479, TRCN0000109478 and TRCN0000109476 (Thermo Fisher), or a scr ctrl shRNA pLKO1-Puro control vector (Thermo Fisher)). These were mixed in 100 µl of Opti-MEM (Thermo Fisher), 6 μl X-tremeGENE 9 was added, and the transfection solution applied to the cells. After overnight incubation, the medium was replaced with fresh DMEM/10%FBS medium, and incubated for another 24 hrs, after which the virus-containing medium was collected and filtered using syringe-driven filters (Millipore Ltd., Livingstone, UK). Filtered virus was added to EpH4 cells in a 6-well plate, incubated for 4 hrs at 37 °C in a 5% CO2 incubator, topped up with DMEM/10% FBS medium + 8 ug/ml polybrene (Sigma) and finally incubated for 24 hrs.
The medium was replaced with fresh medium containing 3 µg/ml puromycin (Sigma) for selection of transduced cells. Cells were routinely passaged with puromycin-medium to maintain the selection.
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9

Recombinant Expression of RNF219-C Fragment

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An MBP-tagged C-terminal fragment of RNF219 (residues 434-726) was produced in Spodoptera frugiperda Sf21 insect cells using the MultiBac baculovirus expression system as previously described25 (link). In brief, the Sf21cells were grown to a density of 2 × 106 cells/ml at 27 °C in Sf900II medium (Thermo Fisher Scientific), infected with the V1 RNF219-C stock of baculovirus, and harvested 48 h after they stopped dividing. Cells were resuspended in lysis buffer (50 mM HEPES, 500 mM NaCl, pH 7.5) and lysed using a Branson Ultrasonics Sonifier SFX550. The lysate was cleared by centrifugation at 40,000 g for 1 h at 4 °C and filtered through 0.45 µm syringe-driven filters (Millipore). The cleared and filtered lysate was diluted to 250 mM NaCl before it was loaded onto a 5 ml MBPTrap column (Cytiva). The bound protein was eluted in one step with binding buffer (50 mM HEPES, 200 mM NaCl, pH 7.5) supplemented with 30 mM maltose.
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