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Brilliant green

Brilliant green is a synthetic dye used as a bacteriostatic agent and biological stain.
It is effective against gram-positive bacteria, and has applications in microbiology, histology, and topical antiseptic preparations.
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Most cited protocols related to «Brilliant green»

For each transcript a standard curve was constructed using the purified PCR product generated for each specific primer pair. Single reactions were prepared for each cDNA along with each serial of dilution using the Brilliant® SYBR® Green Master Mix (Stratagene). Each PCR reaction also included a reverse transcription negative control (without reverse transcriptase) to confirm the absence of genomic DNA, a non template negative control to check for primer-dimer and a porcine genomic DNA control to verify no specific amplification with the primers. Each reaction consisted of 20 μl containing 2 μl of cDNA and 5 pmol of each primer. The real time qPCR was run on MX3000p (Stratagene). The cycling conditions were 1 cycle of denaturation at 95°C/10 min, followed by 40 three-segment cycles of amplification (95°C/30 sec, 58°C–63°C (gene depending, see table 2)/1 min, 72°C/30 sec) where the fluorescence was automatically measured during PCR and one three-segment cycle of product melting (95°C/1 min, 55°C/30 sec, 95°C/30 sec). The baseline adjustment method of the Mx3000 (Stratagene) software was used to determine the Ct in each reaction. A melting curve was constructed for each primer pair to verify the presence of one gene-specific peak and the absence of primer dimmer. All samples were amplified in duplicates and the mean was used for further analysis.
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Publication 2007
brilliant green DNA, Complementary Fluorescence Genes Genome Oligonucleotide Primers Pigs Reverse Transcription RNA-Directed DNA Polymerase Technique, Dilution
All cell cultures were maintained at 37 °C, 5% CO2. hES and iPS cells (HUES3 (control), male; H9 (control), female; HS001 (ALS-SOD1 N139K), male; LWM002 (ALS-SOD1 A4V), female; MBN007 (ALS-SOD1 A4V), female; TM008 (ALS-SOD1 A4V), female; DCM009 (ALS-SOD1 V148G), male; 10013.13 (control), male) were maintained on gelatinized tissue-culture plastic on a monolayer of irradiated CF-1 mouse embryonic fibroblasts (MEFs; GlobalStem), in hESC media, consisting of Dulbecco’s Modified Eagle Medium: nutrient mixture F-12 (DMEM/ F:12, Invitrogen) with 20% Knockout Serum Replacer (KSR; Invitrogen), 110 µM β-mercaptoethanol (BME; Sigma), L-Glutamine and non essential amino acids (NEAA; Invitrogen), and 20 ng/ml basic fibroblast growth factor (bFGF; Invitrogen) (Cowan et al., 2004 (link)). Media was changed every 24 hours and lines were passaged with dispase (Gibco, 1 mg/mL in hES media for 15–30min at 37 °C).
To generate motor neurons, undifferentiated hESCs were passaged using dispase (1 mg/mL) and triturated into small, 50- to 100-cell clumps and placed into ultra-low adherent culture dishes (Corning). For the first three days, cells were kept in suspension in hESC medium, supplemented with 10 µM Rho-associated kinase inhibitor Y27632 (Ascent Scientific) to enhance single cell survival (Watanabe et al., 2007 (link)), 20 ng/mL bFGF (Invitrogen) to enhance growth and 10 µM SB435142 (SB, Sigma) and 0.2 µM LDN193189 (LDN, Stemgent) for neuralization. At day 3, eymbroid bodies (EBs) were switched to neural induction medium (DMEM/F:12 with L-glutamine, NEAA, penicillin/streptomycin, heparin (2 µg/ml), N2 supplement (Invitrogen). At day 5, all-trans retinoic acid (RA; 0.1 or 1 µM, Sigma), ascorbic acid (0.4 µg/ml, Sigma), and BDNF (10 ng/mL, R&D) were added. Dual ALK inhibition (SB+LDN) was pursued until day 7. Hedgehog signaling was initiated on day 7 by application of either C25II modified SHH (R&D), at the standard concentration of 200 ng/ml, a human Smo agonist (HAG, 1 µM, gift from Lee Rubin (Boulting et al., 2011 (link); Dimos et al., 2008 (link))), mouse Smo agonist 1.3 (SAG, 1 µM, (Boulting et al., 2011 (link); Frank-Kamenetsky et al., 2002 (link); Wada et al., 2009 (link); Wichterle et al., 2002 (link))), or purmorphamine (PUR, 1 µM, (Li et al., 2008 (link); Sinha and Chen, 2006 (link)), Stemgent). At day 17, basal medium was changed to Neurobasal (Invitrogen), containing all previous factors and with the addition of 10 ng/mL each of IGF-1, GDNF, and CNTF (R&D), plus B27 (Invitrogen). At day 20 or 30, EBs were dissociated with 0.05% trypsin (Invitrogen), and plated onto poly-lysine/laminin-coated 8-well chamber slides (BD Biosciences) at 0.2–0.5.106 cells/well, and/or 15-mm coverslips at 0.5.106. Plated neurons were cultured in the same medium with the addition of 25 µM BME, and 25 µM glutamic acid (Sigma), and fixed 1 day later.
For immunocytochemistry assays, cultures were fixed for 30 minutes with 4% PFA in phosphate buffered saline (PBS) at 4 °C, washed 3 times for 5 min in PBS, quenched and permeabilized in wash buffer (PBS, 0.1% Triton X-100) plus 50 mM glycine for 15 min. For the EB outgrowth RALDH2 staining, samples were fixed for 10 minutes at room temperature with 4% PFA/10% sucrose pre-warmed to 37°C. Samples were blocked with wash buffer plus 10% normal donkey serum for 1 hr and incubated with primary antibody (Table 1) overnight. Cells were then washed, incubated with DyLight coupled donkey primary anti secondary antibodies (Jackson Immunoresearch, 1:1,000). Finally, cells were washed and counterstained with DAPI (Invitrogen).
Quantitative image analysis of differentiated neuronal cultures was performed using the Multi-Wavelength Cell Scoring module in MetaMorph© software (Molecular Devices). Briefly, EBs were dissociated enzymatically and plated in the presence of neurotrophic factors at densities for which cell overlap was minimal. Following immunostaining, images of at least 9 randomly selected fields (>15,000 cells in total) for each condition were captured using a pre-programmed automated microscope stage. Images were analyzed using the “Multi-Wavelength Cell Scoring” module of the MetaMorph© software, using parameters pre-defined to count only unambiguous bright labeling for each antigen. Intensity thresholds were set while blinded to sample identity, to selectively identify positive cells that displayed unambiguous signal intensity above local background. These parameters were used on all samples in a given experiment, and only minimally adjusted for different staining batches as necessary. Script and Parameter files are available upon request (typically, a cell was ~5,000 grey levels above background to be called positive for any nuclear marker, and was ~10,000 for cytoplasmic markers). A minimum of 15,000 cells per sample was analyzed. All samples were imaged using 10× or 20× objectives on a Zeiss AxioObserver with a Coolsnap HQ2 camera (Photometrics). Some images were acquired using a structured illumination technique using an Apotome module (Zeiss) to achieve 1.9 µm optical sections to ensure co-localization of labeling. For the figures, the brightness and contrast of each channel of an image were adjusted in an appropriate manner to improve clarity.
For Ca2+ imaging experiments utilizing the Hb9::GFP reporter, stem cells were differentiated under the motor neuron differentiation protocol described above, dissociated at day 21 or day 31 and FACS-sorted based on GFP intensity with a 5 laser ARIA-IIu ROU Cell Sorter configured with a 100 µm ceramic nozzle and operating at 20 psi, BD BioSciences. The H9 assays were comprised of mixed neuronal cultures, which a parallel coverslip was stained and quantified to have 53% HB9/ISL1+ motor neurons. All cultures were plated onto 15–25 mm diameter coverslips at a density of 100,000–150,000 cells per coverslip in day 17+ neurobasal media with factors described above with the addition of 0.5 µM EdU, and matured 6 days prior to Ca2+ imaging. Cells were loaded with 3 μM Fluo-4 AM (Invitrogen, Carlsbad, CA) dissolved in 0.2% dimethyl sulfoxide/0.04% pluronic acid (Sigma) in HEPES-buffered physiological salt solution (PSS) for 1 hour at room temperature. PSS contained (mM): NaCl 145, KCl 5, HEPES 10, CaCl2 2, MgCl2 2 and glucose 5.5, pH 7.4. Cultures were continuously superfused with PSS at a rate of approximately 0.5 ml/minute. The cultures were imaged using a 10× objective on an inverted epi-fluorescent Zeiss AxioObserver microscope, equipped with a Coolsnap HQ2 camera (Photometrics). For imaging spontaneous Ca2+ transients, single sets of 200–300 images were acquired at a rate of approximately 2 Hz from each coverslip. For the kainate experiments, 36 images were acquired at a rate of 0.033 Hz and the superfusing PSS was replaced with PSS containing kainate (100 μM) for 60 seconds. Image analysis was performed using ImageJ (http://rsb.info.nih.gov/ij/) or AxioVision 4.7 (Zeiss). Ca2+ transients were determined from regions of interest encompassing the soma of individual cells. A minimum of two cultures obtained from a single differentiation of each cell line and each time point were used for the kainate and all Ca2+ imaging experiments.
For whole cell patch clamp recordings, S+P differentiated HUES3 Hb9::GFP cells were plated on polyornithine/laminin-coated 25 mm diameter coverglass at density of 50,000 per coverslip and cultured for 7 days in the presence of 0.5 µM EdU prior to recording (i.e. DIV 21+7). Current clamp recordings were carried out using an Axopatch 2B amplifier. Data were digitized using a Digidata 1322A digital to analogue converter and were recorded at a 10 KHz sample rate using pClamp 10 software (all equipment from Molecular Devices). Patch pipettes were fabricated using a P-97 pipette puller (Sutter Instruments). The external recording solution contained (in mM), 145 NaCl, 5 KCl, 10 HEPES, 10 glucose, 2 CaCl2, 2 MgCl2. The pH was adjusted to 7.3 using NaOH and the osmolality adjusted to 325 mOsm with sucrose. The pipette solution contained (in mM): 130 CH3KO3S, 10 CH3NaO3S, 1 CaCl2, 10 EGTA, 10 HEPES, 5 MgATP, 0.5 Na2GTP, pH 7.3, 305 mOsm. Experiments were carried out at room temperature (21 – 23 °C). During recordings, current was injected to hold the cells at approximately −60 mV. Action potentials were evoked using incrementally increasing current steps 1 s in duration. The maximum amplitude of the current step (20 – 50 pA) and the size of the increment was calculated based on the input resistance of the cell.
To perform xenotransplantations day 21 EBs from HUES3 Hb9::GFP under the ventralization with SAG+PUR were collected and placed into L-15 media (Invitrogen) containing penicillin/streptomycin (GIBCO). Transplantation was performed as previously described (Wichterle et al., 2002 (link)). Briefly, after a small suction lesion at the prospective intraspinal site was created in a chick embryo at stage 15–18 at somites 15–20, lightly triturated EBs were loaded into a handheld micro-injector. The EBs was placed into the lesion. After 48 hours, the chicks were sacrificed, fixed with 4% PFA for 2 hours at 4°C, and neurite outgrowth and cell body placement was accessed by cutting 200 µm vibratome sections (n = 2), and by cutting 30 µm sections along the spinal cord (n = 5).
Human fetal spinal cords were collected in accordance with the national guidelines of the United States (NIH, FDA) and the State of New York and under Columbia University institutionally approved ethical guidelines relating to anonymous tissue. The fetal material was obtained after elective abortions, and was classified on the basis of external morphology according to the Carnegie stages. Gestational age was determined by last menstrual period of the patient or by ultrasound, if the ultrasound estimate differed by more than one week as indicated by the obstetrician. The spinal cord was removed as intact as possible prior to fixation with fresh, cold 4% PFA for 1.5 hours on ice. Post fixation, the cord was measured and cut into 3 anatomical sections to accommodate embedding in OCT Compound (Tissue-Tek, Redding, CA) and stored at −80 °C prior to cutting on a microtome. 12µm sections were cut along the full length of the cord, taking care to have all 3 sections on each slide in 7 independent sections. This allowed for full analysis and internal staining controls since each slide had cervical, brachial, thoracic and lumbar sections that clearly showed staining within the various motor columns present at different rostal-caudal levels of the spinal cord.
cDNA was obtained from 50,000 FACS purified MN’s from either day 21 S+P (methods described above), or from RA/SHH MN’s at day 31. cDNA preparation was carried out using commercially available kits following the manufacturer’s instructions: RNA isolation (Trizol LS; Invitrogen), cDNA by Brilliant II SYBR green (Stratagene) without amplification. All samples were processed in parallel on the same qPCR plate.
primers:ForwardReverse
RALDH2TTTTGCTGATGCTGACTTGGGCAGCACTGACCTTGATTGA
FOXP1TGACCTTTTGAGGTGACTATAACTGTGGCTGAACCGTTACTTTTTG
LHX3GTTCAGGAGGGGCAGGACCCCAAGCTCCCGTAGAGG
CHT1AAGCCATCATAGTTGGTGGCCGAGCCAAGCTAGGCCATAACCTGGTAC
HOXA5CAGCACCCACATCACGGAGAGGCAAAGA
HOXC6CCAGGACCAGAAAGCCAGTAGTTAGGTAGCGATTGAAGTGAAA
HOXC8CTTCGCTGTTTGATTTCTATTCTGTACGCTGGAGGTTTCTTTCTTT
HOXD9TCGCTGAAGGAGGAGGAGACAAACACCCACAAAGGAAAAC
STD qPCR amplification: 95°- 30”, 55°-60”, 72°-45”
For paired-end RNA-Seq experiments, 400 ng of total RNA was prepared after FACS purification of 500,000 GFP+ or GFP cells. The RNA samples were then amplified using a NuGEN RNA kit for genomic sample amplification, and sequenced to a depth of 21 (S+P) and 35 (SHH) million paired-end reads on an Illumina HiSeq instrument at the HudsonAlpha Institute of Biotechnology. The reads were aligned to the reference transcriptome as well as a library of exon junctions using Bowtie (Version 1) (Langmead et al., 2009 (link)). Data was analyzed using Expression Plot (Friedman and Maniatis, 2011 (link)) using a P value of 0.001 and a 2 fold change threshold. Gene ontology was performed using DAVID (Huang et al., 2008 , 2009 (link)) with enrichment sets from Expression Plot. The RNA-seq data is available in the Gene Expression Omnibus (GEO) database (http://www.ncbi.nlm.nih.gov/geo/) under the accession number GSE41795.
All quantitative data was analyzed using Sigma Plot 11 or Microsoft Excel. Sample groups were subject to Student’s t-test or where appropriate a One-Way ANOVA with Holm-Sidak post hoc pair-wise comparisons was performed. All experimental data passed an equal variance and normality test (Shapiro-Wilk).
Publication 2013
An aliquot of 0.5 μg total RNA was treated with 1 unit DNAse (Fermentas, St. Leon-Rot, Germany) 30 min at 37°C. Reverse transcription of RNA (0.5 μg) was performed with oligo (dT)12–18 primer and 200 units of SUPERSCRIPT II (Invitrogen, Karlsruhe, Germany) and 24 units of Ribo LockTM RNAse inhibitor (Fermentas) for 1 h at 42°C. The cDNA was used for PCR analysis. All cDNA probes were analyzed for: ACTA1, (NM_001100), amplicon length 85 bp; MYOG, (NM_002479), amplicon length 113 bp; MYH3, (NM_002470), amplicon length 84 bp and the RG: ACTB (NM_001101), amplicon length 104 bp; B2M, (NM_004048), amplicon length 98 bp; GAPDH, (NM_002046), amplicon length 119 bp; cyclophilin A/PPIA, (NM_203430), amplicon length 121 bp; RPLPO, (NM_001002), amplicon length 170 bp; TBP, (NM_003194), amplicon length 132 bp. The QuantiTect/PrimerAssays were purchased from QIAGEN GmbH (Hilden, Germany). cDNAs were amplified with Brilliant® II SYBR® Green QRT-PCR Master Mix (Stratagene-Agilent Technologies, Waldbronn, Germany). The thermal profile consisted of 1 cycle at 50°C for 2 minutes followed by 1 cycle at 95°C (2 min), 45 cycles at 95°C (15 sec), 60°C (1 min). Amplification was performed using the Mx3005P™ QPCR System (Stratagene). For relative quantification, a standard curve was generated in every individual run. Shortly, total RNA was pooled from muscle biopsies of healthy human volunteers, reverse transcription was performed and a serial dilution of the cDNA was used to perform the calibration curve. The data were analyzed using the relative standard curve method. For each unknown sample, the relative amount is calculated using linear regression analysis from their respective standard curves. Data were analyzed using the Mx3005P analysis software (Stratagene-Agilent Technologies, Waldbronn, Germany). The efficiencies of all GOI and RG were calculated in every individual run (Table 1).
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Publication 2009
Biopsy Cyclophilin A Deoxyribonuclease I DNA, Complementary Endoribonucleases GAPDH protein, human Healthy Volunteers Homo sapiens Muscle Tissue Oligonucleotide Primers Oligonucleotides Reverse Transcription SYBR Green II Technique, Dilution
Stable RNAi was achieved by viral shRNA. For Sec10 knockdown, cells were transfected with siRNA oligonucleotides as described6 (link). In all instances knockdown was verified by standard western blot or Q-RT PCR procedures (Brilliant-II SYBR Green Kit, Agilent, Santa Clara, CA), normalizing to GAPDH expression. Q-RT PCR Primers are presented in Supplementary Table 1. RNAi target sequences are presented in Supplementary Table 2. Rab8a_1, Rab10, Rab11a_1, Rab11b, in pRVH1-puro or –hygro retroviruses were previously published44 (link). All other shRNAs were generated in pLKO.1-puro45 (link), or pLKO.1-blast, which was constructed by exchanging the puromycin resistance gene for blasticidin. Cdc42, Par3 and Tuba shRNAs were adapted for pLKO.1 from published sequences21 (link), 46 (link). pLKO.1 lentiviruses were constructed according to the Addgene pLKO.1 protocol (www.addgene.org) using iRNAi (www.mekentosj.com), and target sequences were based on an (AA)N19 algorithm. RNAi sequences were submitted to BLAST (NCBI) to verify target specificity. For isoform-specific RNAi to Rabin8, shRNAs predicted to target the α isoform (Rabin8_4, Rabin8_5) or to both α and β (Rabin8_2) isoforms of canine Rabin8 were extrapolated from sequence alignment with human Rabin8 splice forms (mined from NCBI). For knockdown and rescue experiments, GFP-tagged plasmids of transcripts from human or rat, which are not targeted by anti-canine shRNAs, were used.
Publication 2010
alpha-Tubulin brilliant green Canis familiaris CDC42 protein, human Cells GAPDH protein, human Genes Homo sapiens Lentivirus Oligonucleotide Primers Oligonucleotides Plasmids Protein Isoforms Puromycin RAB8A protein, human Retroviridae Reverse Transcriptase Polymerase Chain Reaction RNA, Small Interfering RNA Interference Sequence Alignment Short Hairpin RNA Western Blotting
Expression Constructs—The pGW1H-Irga6cTag1 construct was
generated by amplification of the Irga6cTag1 sequence from
pGEX-4T-2-Irga6cTag1 (former pGEX-4T-2-IIGP-m)
(16 (link)) by using Irga6cTag1
forward (5′-cccccccccgtcgaccaccatgggtcagctgttctcttcacctaag-3′) and
reverse (5′-cccccccccgtcgactcagtcacgatgcggccgctcgagtcggcctag-3′)
primers and cloned into pGW1H vector (British Biotech) by SalI digestion.
Mutations were introduced into the coding region of pGW1H-Irga6wt
(15 (link)), pGW1H-Irga6cTag1, and
pGEX-4T2-Irga6wt (16 (link))
according to the QuikChange site-directed mutagenesis kit (Stratagene) using
the following forward and corresponding reverse primers: G2A,
5′-gagtcgaccaccatggctcagctgttctcttca-3′; Δ7-12,
5′-gggtcagctgttctctaataatgatttgccc-3′; Δ7-25,
5′-ccaccatgggtcagctgttctctaaatttaatacggg-3′; Δ20-25,
5′-gaataatgatttgccctccagcaaatttaatacgggaag-3′; F20A,
5′-gagaataatgatttgccctccagcgctactggttattttaag-3′; T21A,
5′-gaataatgatttgccctccagctttgctggttattttaag-3′; G22A,
5′-gccctccagctttactgcttattttaagaaatttaatacggg-3′; Y23A,
5′-gccctccagctttactggtgcttttaagaaatttaatacggg-3′; F24A,
5′-gccctccagctttactggttatgctaagaaatttaatacgggaag-3′; K25A,
5′-gccctccagctttactggttattttgcgaaatttaatacgggaag-3′; K82A,
5′-gggagacgggatcaggggcgtccagcttcatcaataccc-3′; S83N,
5′-ggagacgggatcagggaagaacagcttcatcaataccctg-3′; E106A,
5′-gctaaaactggggtggtggcggtaaccatggaaag-3′.
Cell Culture and Serological Reagents—L929 (CCL-1) and gs3T3
(Invitrogen) mouse fibroblasts were cultured in IMDM or Dulbecco's modified
Eagle's medium (both GIBCO) supplemented with 10% fetal calf serum (Biochrom).
Hybridoma 10D7 and 10E7 cells were grown in IMDM, supplemented with 5% fetal
calf serum. Cells were induced with 200 units/ml IFNγ (Cell Concepts)
for 24 h and transfected using FUGENE6 transfection reagent according to the
manufacturer's protocol (Roche Applied Science). Propagation of T.
gondii
strain ME49 was done as described previously
(8 ). gs3T3 cells were infected
for 2 h with T. gondii ME49 strain at a multiplicity of infection of
8 24 h after IFNγ stimulation. The following serological reagents were
used: anti-Irga6 mouse monoclonal antibodies 10D7 and 10E7, anti-Irga6 rabbit
polyclonal serum 165, anti-cTag1 rabbit polyclonal serum 2600
(8 ), donkey-anti-mouse Alexa
546, donkey anti-rabbit Alexa 488 (all from Molecular Probes), goat anti-mouse
κ light chain (Bethyl), goat anti-mouse κ light chain horseradish
peroxidase (Bethyl), goat anti-mouse κ light chain-fluorescein
isothiocyanate (Southern Biotech), 4′,6-diamidino-2-phenylindole (Roche
Applied Science), and donkey anti-rabbit, donkey anti-goat, and goat
anti-mouse horseradish peroxidase (all from Amersham Biosciences).
Antibody Purification and Papain Digestion—10D7 and 10E7
antibodies were purified from corresponding hybridoma supernatants over a
Protein A-Sepharose column (Amersham Biosciences). Antibody was eluted with 50
mm sodium acetate, pH 3.5, 150 mm NaCl and
pH-neutralized to 7.5 with 1 m Tris, pH 11. Buffer was exchanged
five times subsequently by dilution of antibody-containing sample in papain
buffer (75 mm phosphate buffer, pH 7.0, 75 mm NaCl, 2
mm EDTA) and concentrated in a centrifugal concentrator
(Vivaspin20; Sartorius) with a 10 kDa cut-off filter at 2000 ×
g at 4 °C. The concentration of the antibodies was determined by
using formula, concentration of antibody (mg/ml) = 0.8 ×
A280. Papain digestion was done according to Ref.
20 (link). The papain-digested
antibodies were further purified on a HiLoad 26/60 Superdex 75 preparation
grade column (Amersham Biosciences) in papain buffer. Samples were incubated
in SDS-PAGE sample buffer under nonreducing conditions and subjected to
SDS-PAGE. Proteins were detected by colloidal Coomassie staining.
Treatment with Aluminum Fluoride—AlCl3 (Sigma)
was added to 10 ml of IMDM containing no fetal calf serum to a final
concentration of 300 μm and mixed by vigorous shaking.
Subsequently, NaF (Sigma) was added to a final concentration of 10
mm and mixed, and the final solution was applied to confluent L929
cells previously induced with IFNγ or transfected for 24 h. Cells were
incubated in aluminum fluoride complex (AlFx) solution for 30 min at 37 °C
and then washed with cold PBS and collected by scraping. Cell pellets were
lysed in 0.1% Thesit/PBS containing 300 μm AlCl3 and
10 mm NaF in the presence or absence of 0.5 mm GTP for 1
h at 4 °C.
Immunoprecipitation and
Immunofluorescence
—Immunoprecipitation was modified from Ref.
21 . 1 × 106 L929 fibroblasts/sample were induced with IFNγ and/or transfected for 24
h (or left untreated) and harvested by scraping. Cells were lysed in 0.1%
Thesit, 3 mm MgCl2, PBS, Complete Mini protease
inhibitor mixture without EDTA (Roche Applied Science) for 1 h at 4 °C in
the absence of nucleotide or in the presence of 0.5 mm GDP, GTP,
GTPγS, or 300 μm AlCl3 and 10 mm NaF
in the presence or absence of 0.5 mm GTP (all from Sigma). Protein
A-Sepharose™ CL-4B beads (Amersham Biosciences) were incubated with 10D7
monoclonal mouse anti-Irga6 antibody or 2600 (anti-cTag1) polyclonal rabbit
serum for 1 h at 4 °C. Bound proteins were eluted by boiling for 10 min in
elution buffer (100 mm Tris/HCl, pH 8.5, 0.5% SDS) with SDS-PAGE
sample buffer (50 mm Tris/HCl, pH 6.1, 1% SDS, 5% glycerol, 0.0025%
bromphenol blue (w/v), 0.7% β-mercaptoethanol). Immunofluorescence was
preformed as previously described
(15 (link)).

10D7 antibody detects Irga6 at the PVM but not at the ER. gs3T3
fibroblasts were induced with IFNγ for 24 h prior to 2-h infection with
T. gondii ME49 strain with a multiplicity of infection of 8. Irga6
protein was labeled with rabbit anti-Irga6 polyclonal serum 165 (red)
and with mouse monoclonal anti-Irga6 antibodies 10E7 (A) or 10D7
(B) (green). PC, phase-contrast images.
Parasitophorous vacuoles are indicated by the arrowheads. 10D7
detected Irga6 on the PVM efficiently but the cytoplasmic, ER
membrane-associated Irga6 at a barely detectable level.

Colloidal Coomassie Staining—Gels were washed 30 min with
H2O and subsequently placed in incubation solution (17% ammonium
sulfate (w/v), 20% MeOH, 2% phosphoric acid). After a 60-min incubation, solid
Coomassie Brilliant Blue G-250 (Serva) was added to the solution to a
concentration of 330 mg/500 ml and incubated 1-2 days. The gels were destained
by incubation in 20% MeOH for 1 min and stored in 5% acetic acid. All was done
at room temperature and while shaking.
Expression and Purification of Irga6 Proteins from E.
coli
—pGEX-4T-2-Irga6 constructs were transformed into BL-21 E.
coli
strain. Cells were grown at 37 °C to an A600 of 0.8 when the expression of glutathione S-transferase-fused Irga6
proteins was induced by 0.1 mm isopropyl-β-d-thiogalactoside at 18 °C overnight. Cells
were harvested (5000 × g, 15 min, 4 °C); resuspended in
PBS, 2 mm DTT, Complete Mini protease inhibitor mixture without
EDTA (Roche Applied Science) and lysed using a microfluidizer (EmulsiFlex-C5;
Avestin) at a pressure of 150 megapascals. The lysates were cleared by
centrifugation at 50,000 × g for 60 min at 4 °C. The
soluble fraction was purified on a glutathione-Sepharose affinity column
(GSTrap FF 5 ml; Amersham Biosciences) equilibrated with PBS, 2 mm dithiothreitol. The glutathione S-transferase domain was cleaved off
by overnight incubation with thrombin (20 units/ml; Serva) on the resin at 4
°C. Free Irga6 was eluted with PBS, 2 mm dithiothreitol, and
the protein content in fractions was analyzed by SDS-PAGE and visualized by
Coomassie staining (22 (link)). The
protein-containing fractions were concentrated in a centrifugal concentrator
(Vivaspin20; Sartorius). Aliquots were shock-frozen in liquid nitrogen and
stored at -80 °C. The concentration of protein was determined by UV
spectrophotometry at 280 nm.
Publication 2008

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Publication 2024
For the photocatalytic degradation study, three dyes were selected such as Orange G, Acid Blue 161, and Brillant Green. To eliminate the maximum dye level, a Pen‐Ray UV (ColeParmer) lamp with a wavelength of 254 nm and a light intensity of 44 W m−2 was used. The saturated oxygen concentration in the solution medium was achieved with the help of a pump. Experiments were made by adding 100 mg of photocatalyst to a 20 mg L−1 dye solution with a volume of 400 mL. Before starting the experiments, they were mixed for 30 min in the dark for the adsorption and desorption of dye molecules on the surface of the photocatalysis. Samples taken at different time intervals were centrifuged to determine the concentration. The concentration of the samples was measured at wavelengths of 578, 624, and 475 nm using a UV spectrophotometer (Optizen α). Table 1 shows the molecular properties of Brilliant Green, Acid Blue 161, and Orange G dyes. Decomposition percentages of Acid Blue 161, Brilliant Green, and Orange G dyestuffs before and after photocatalytic degradation were calculated using Equation 1.
Percentageofdegradation%=C0Cs/C0×100
C0 and Cs represent the initial and final dye concentrations in the aqueous phase, respectively.
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Publication 2024

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