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12 protocols using rat anti ha mab 3f10

1

Immunoblot Analysis of Parasite Proteins

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Parasite samples were centrifuged at 500 g for 5 min at room temperature (RT), and pellets were stored at −20°C until the time of protein extraction. To isolate parasites from RBCs, the pellets were thawed and resuspended in 0.15% saponin for 5 min at RT. Lysed RBCs were removed by washing three times with PBS. Parasite pellets were resuspended in NuPAGE LDS sample buffer (Thermo Fisher) containing 2% β‐mercaptoethanol and incubated at 95°C for 5 min. Proteins were resolved by SDS–PAGE on 4–12% gradient gels and transferred to nitrocellulose membranes. To detect EcDPCK‐mCherry constructs, membranes were blocked in 5% milk and probed overnight at 4°C with 1:10,000 rabbit anti‐mCherry (vide supra). They were then incubated for an hour at RT with 1:10,000 donkey anti‐rabbit HRP‐linked secondary antibodies (GE healthcare, NA934). Protein bands were detected on X‐ray film using SuperSignal West Pico Chemiluminescent Substrate (Thermo Scientific), according to the manufacturer’s protocol. Membranes were stripped of antibody with 200 mM glycine (pH 2.0) for 5 min and probed with 1:2,500 rat anti‐HA mAb 3F10 (Roche) in order to detect api‐SFG which contains a C‐terminal HA tag (Swift et al,2020b (link)). After incubation with 1:5,000 goat anti‐rat HRP‐linked secondary antibodies (GE healthcare, NA935), proteins were detected as described above.
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2

Multimodal Imaging of Parasite Organelles

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For mitochondrial staining, the parasite culture was treated with 75 nM MitoTracker Red CMX-Ros (Invitrogen) for 30 min in fresh media prior to fixation. All cultures were fixed in 4% paraformaldehyde–0.0075% glutaraldehyde on polylysine-treated slides for 30 min. Cells were permeabilized for 10 min in 1% Triton X-100, remaining aldehydes were reduced with 0.1 mg/ml NaBH4 for 10 min, and cells were blocked for 2 h in 3% BSA. Parasite cytosol was stained with 1:2,000 mouse anti-aldolase, the apicoplast was stained with 1:1,000 rabbit anti-ACP (38 (link)), and lipoamidase was stained with 1:500 rat anti-HA MAb 3F10 (Roche) overnight. After treatment with primary antibodies, the slides were washed and treated with cognate secondary antibodies. The cognate secondary antibodies were 1:2,000 rabbit α-mouse IgG Alexa Fluor 594 (rabbit anti-mouse IgG conjugated to Alexa Fluor 594 diluted 1:2,000), 1:2,000 goat α-rabbit IgG Alexa Fluor 594, or 1:2,000 goat αRat IgG Alexa Fluor 488 (Invitrogen). The slides were washed and mounted with Prolong Gold antifade reagent with DAPI (Invitrogen). Microscopy images were taken with the Zeiss Axio Imager. The PDM channel and PCC values were derived using Volocity software as previously described (39 (link)), and mean PCC values were obtained by analyzing multiple images from two independent experiments for each genotype.
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3

Golgi marker antibody validation

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Rabbit GM130 (also known as GOLGA2, Golgin subfamily A member 2)-specific pAb (HPA021799) was purchased from Sigma Aldrich (St. Louis, MO, USA). Mouse anti-GM130 mAb (clone 35) was from Becton Dickinson and Company (Franklin Lakes, NJ, USA). Anti-Myc-tag mouse ascites fluid (clone 9E10, SAB4300605), mouse anti-Golgi 58 k mAb (G2404), mouse anti-calbindin (C9848), and rabbit anti-SUN1 pAb (HPA008346) were also from Sigma Aldrich. Sheep anti-TGN46 pAb (AHP500G) was from AbD Serotec (Oxford, UK). Anti-SUN2 pAb (#06–1038) was purchased from Millipore (Burlington, MA, USA). Rabbit anti-KIF20A pAb (ab70791) was obtained from Abcam (Cambridge, United Kingdom). Rat anti-HA mAb (3F10) was from Roche (Basel, Switzerland). Rabbit anti-GFP pAb (code No. 598) was from Medical and Biological Laboratories (Aichi, Japan). KIF20A inhibitor, paprotrain, was purchased from Sigma Aldrich and used at a final concentration of 20 µM47 (link).
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4

Lipoamidase Activity Determination

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Parasite pellets as described above were resuspended in RIPA buffer (Boston Bioproducts) to determine lipoamidase activity in cell lysates, and the reaction was quenched by the addition of Laemmli loading buffer. Otherwise, pellets were resuspended in NuPAGE LDS sample buffer (Thermo Fisher) and alternatively vortexed for 1 min and boiled for 4 min, a total of two times. Proteins were resolved by SDS-PAGE on 4 to 12% gradient gels and transferred to nitrocellulose membranes. For autoradiography, membranes were dried overnight, and autoradiography was used to detect 35S-lipoate incorporation. For Western blotting, membranes were blocked and probed with 1:5,000 rat anti-HA MAb 3F10 (Roche) primary antibodies to detect lipoamidase, 1:5,000 rabbit antilipoate (37 (link)) to detect lipoylation of the apicoplast PDH E2 subunit, and either 1:10,000 mouse anti-HSP70 or 1:10,000 mouse antialdolase for loading controls.
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5

Immunostaining of Salivary Gland Chromosomes

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CMTr1 and CMTr2 were expressed in salivary glands with elavC155-GAL4 from a UAS transgene tagged with HA or FLAG, respectively, as described39 (link). Briefly, larvae were grown at 18 °C under non-crowded conditions. Salivary glands were dissected in PBS containing 4% formaldehyde and 1% TritonX100, and fixed for 5 min, and then for another 2 min in 50% acetic acid containing 4% formaldehyde, before placing them in lactoacetic acid (lactic acid:water:acetic acid, 1:2:3). Chromosomes were then spread under a siliconized coverslip and the coverslip was removed after freezing. Chromosome was blocked in PBT containing 0.2% BSA and 5% goat serum and sequentially incubated with primary antibodies (mouse anti-PolII H5 IgM, 1:1000, Abcam, and rat anti-HA MAb 3F10, 1:50, Roche, or rabbit anti-FLAG, 1:1000, SIGMA) followed by incubation with Alexa488- and/or Alexa647-coupled secondary antibodies (Molecular Probes) including DAPI (1 µg/ml, Sigma).
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6

Immunohistochemical Staining of scFvs

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NHS cryosections of 5 µm thickness were blocked with TBS-Ca2+ (Bio-Rad) plus 1% BSA (Sigma-Aldrich) at RT for 30 min. Slides were washed with TBS-Ca2+ three times and incubated with samples diluted in TBS-Ca2+ plus 1% BSA at RT for 60 minutes. Binding of scFvs was detected through staining with rat anti-HA mAb (3F10; dilution, 1:100; Roche), followed by an Alexa Fluor 594-conjugated anti-rat IgG (dilution, 1:200; Invitrogen). Analogously, IIF was performed on ME substrates (SCIMEDX; EUROIMMUN), following above protocol.
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7

Detecting E-cadherin and Associated Proteins

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The following monoclonal antibodies were used to detect E-cadherin: DECMA-1, raised against the extracellular domain of E-cadherin (provided by Rolf Kemler, Max-Planck Institute for Immunobiology), and C20820, a mAb detecting the cytoplasmic domain of E-cadherin (BD Biosciences). For immunoprecipitation, rabbit polyclonal antibodies raised against the extracellular domain of E-cadherin (provided by Rolf Kemler) were used. Rat anti-HA mAb (3F10) was purchased from Roche Molecular Biochemicals (Mannheim, Germany). Mouse anti-FLAG (DYKDDDDK) mAb was purchased from Wako Pure Chemical Industries (Osaka, Japan). Mouse mAbs against α-catenin, β-catenin, and plakoglobin were purchased from BD Biosciences, and mAbs against vinculin and actin were obtained from Sigma-Aldrich. Rabbit anti–non-muscle myosin heavy chain II-A, II-B, and II-C antibodies were obtained from BioLegend (San Diego, USA). All secondary antibodies were obtained from Jackson ImmunoResearch Laboratories (West Grove, USA).
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8

Immunodetection of Cellular Proteins

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Anti-His (H-3) mouse monoclonal antibody (MAb) conjugated with horseradish peroxidase (HRP) and anti-GST MAb (B-14) were purchased from Santa Cruz. Anti-HA rat MAb (3F10) and anti-myc mouse MAb (9E10) conjugated with HRP were purchased from Roche. Anti-flag mouse MAb M2 was obtained from Sigma. Anti-IE1 polyclonal antibody (PAb) was raised in rabbits using the purified IE1 protein. Mouse MAb 8131, which detects epitopes present in both IE1 and IE2 (exons-2 and -3), was purchased from Chemicon (Temecula, CA, USA). Mouse MAbs specific for IE1 (6E1) and IE2 (12E2) were purchased from Vancouver Biotech and mouse MAb against β-actin was purchased from Sigma. Mouse MAb against SRT epitope was previously described [23] (link).
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9

Antibody Purchase and Characterization

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Antibodies were purchased from commercial sources as follows: anti-GFP monoclonal antibody (mAb) (B-2), anti-SBP mAb (SB-19-C4), and anti-KIAA0802 polyclonal antibody (pAb) (W19) (Santa Cruz Biotechnology); anti-α-tubulin mAb (DM1A) and anti-acetylated tubulin mAb (Sigma-Aldrich, St. Louis, MO); anti-V5 mAb, anti-RFP pAb (Invitrogen); anti-RFP mAb (RF5R) (Thermo Fisher Scientific); anti-HA rat mAb (3F10) (Roche Applied Science Indianapolis, IN); anti-GFP pAb (MBL); anti-GM130 mAb (Cell Signaling Technology)
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10

Antibodies for Viral Protein Detection

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Mouse monoclonal antibody (MAb) 810R, which detects epitopes present in both IE1 and IE2, was purchased from Chemicon. Mouse MAbs against UL44 (p52) and UL99 (pp28) were obtained from Virusys. Anti-β-actin and anti-α-tubulin mouse MAbs were purchased from Sigma. Anti-HA rat MAb 3F10 and anti-myc mouse MAb 9E10, conjugated with peroxidase or labeled with fluorescein isothiocyanate (FITC), were purchased from Roche. Anti-ISG15 (F-9) and anti-STAT2 mouse MAbs were obtained from Santa Cruz. Mouse MAb against SRT epitope was previously described [91 (link)]. UBP43 antibody was previously described [92 (link)]. Rabbit polyclonal Ab (PAb) for STAT2 (C-20) and STAT2 phosphorylated at Tyr689 were purchased from Santa Cruz and Upstate, respectively. Rabbit PAb for ISG15 was kindly provided by Chin Ha Chung (Seoul National University, Seoul, Republic of Korea).
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