9 Matching Annotations
  1. May 2019
    1. and fixed with 100μl of fixative solution per well, for 10 minutes at room temperature. The cells were then washed twice with PBS and 100μl of staining solution was added to each well. The plate was kept at 37° C, until the color development.
    2. 4x103-5x103 cells were plated in 96 well plate, well. Cells were transfected with reporter plasmid 18 -24 hrs after plating. After 48 hrs, cells were washed once with PBS
    3. This protocol is for the detection of β-gal expression in fixed cells. It was performed on 96-well plates for initial screening of tTA transfected clone, and is a modification of Sanes et al., 1986
    1. Cells grown overnight in YNBmedium wereinoculated in fresh YNB mediumand incubated at 30 ̊C with shaking at 200 rpm. Cells were harvested when the cell density reached to an OD600of 0.6-0.8.Cells were consecutively washed with sterile MQ water and YNB without phosphate (YNB-Pi) medium. Washed cells were inoculated either in YNB orYNB-Pimediumto the initial OD600of 0.1. Cells were incubated at 30 ̊C for 3-4 h, harvested and resuspendedin 100 μlYNB-Pimedium. Radioactive P32-labelled o-phosphoric acid(Jonaki# LCP 32)was added to the cell suspension to a final concentration of 1 μCi/mlandcells were incubated for 30 min.For determining phosphate uptake, a10-12 μl cell suspensionaliquot,after every5 min,was removed and kept on ice.To this cell suspension, 500 μl ice-cold YNB-Pimediumwas addedand cells were harvested by centrifugation at 5,000 g for 5 minat 4 ̊C.These cells were washed with ice-cold YNB-Pimedium thrice and resuspendedin 100 μlPBS(1X). 10-20 μl of this cell suspension was added to5 ml scintillation fluid and β-decay counts were measured in ascintillation counter(Tri-Carb 2910 TR Liquid Scintillation Analyzer, PerkinElmer).Scintillation counts were normalized to total cell number and plotted with respect to time. Total phosphateuptake was expressed as P32c.p.m/OD600cellswhere c.p.m refers tocounts per min
    1. To preclude the possibility of human RNA contamination, cDNA prepared from internalized yeast was examined for the presence of human transcripts encoding Ccl5 and histone H3. However,no amplification forhuman genes was observed, thus, eliminating any possiblecontamination of THP-1 RNA with yeast RNA
    2. Primersfor real-timePCR analysisweredesigned using Primer3 plus software and are listed in Table 4. To extractRNA from macrophage-ingested C. glabratacells, infected THP-1cells were washed twice with PBS and lysed in 1 ml ice-cold water. Lysate was centrifuged followed by two quick washes with DEPC-treated water andwashed yeast cell pellets were frozen on dry ice.For RNA extraction, yeast cells were disrupted with glass beads in trizol and total RNAwas isolated usingacid phenol extraction method described above.Optimal primer and cDNA concentrations were standardizedand qRT-PCR was performedusing ABI 7500 Fast Real-Time PCR System (Applied Biosystems).In brief, 0.5 μl cDNA,0.1 to 0.2picomoles of gene specific primers and 10 μl 2X MESA GREENqPCR™ Mastermix Plus containing SYBR green dye (Eurogentec)were mixed in thewellsof a 96-well PCRplate (Axygen). Final reaction volume was adjusted to 20 μl with DEPC-treated water. Transcript levels were quantified with an end-point value known as Ct(cyclethreshold). Expression of TDH3, which encodes CgGapdh,was used asaninternal control. The Ct defines the number of PCR cycles required for the fluorescent signalof SYBR green dye to cross beyondthe background level.Fold-change in transcript expression was determined usingfollowing formula.Fold change in expression = 2-ΔΔCtΔΔCt= ΔCttreated -ΔCtuntreatedΔCttreated = Ctvalue forthe gene of interest under treated condition -Ctvalue forthe internal control gene (TDH3) under treated conditionΔCt untreated = Ctvalue forthegene of interest under untreated condition -Ctvalue forthe internal control (TDH3) gene under untreated condition
    1. Ferric-iron-reduction activity of Xanthomonas oryzaepv. oryzicolawas measured using ferrozine, a chromogenic ferrous iron chelator, as described previously (Velayudhan etal., 2000; Worst et al., 1998). For estimating the ferric reductase activity, Xanthomonas oryzaepv. oryzicolastrains were grown in 20 ml PS medium carrying appropriate antibiotics for 24 h to OD600 of 1. Cell free PS media was incubated under similarcondition to be used as control. Chromogenic ferrous iron chelator, ferrozine was added to a final concentration of 1 mM, and FeCl3was added as ferric iron source to a final concentration of 50 μM, and incubated at 28ºC. At regular time intervals, 1 ml aliquotes were taken from the test culture and control, centrifuged to remove the cells, and absorbance of the magenta coloured Fe2+-ferrozine complex in the cell free culture supernantant was measured at 535 nm by using control supernatant as reference. The Fe2+reduction activity was quantified as micromoles of Fe2+-Ferrozine complex formed
    1. To perform immunoblotting or western blotting, appropriate amounts of total protein(ranging from 20-40 μg) were separated ona SDS-PAGE gel of 12%acrylamide concentration in Tris-Glycine-SDS gel running buffer. Protein separation was done at 70-100 V for 2-3 h using a MINI PROTEAN®3 electrophoresis unit (Bio-Rad). Followingseparation, proteins weretransferredto polyvinylidene difluoride (PVDF) membrane, using a Bio-Rad Mini Trans-Blot electrophoretic transfer unit in Tris-Glycine transfer buffer at 4⁰C. Before setting transfer assembly, PVDF membrane was first activated in 100% methanolfollowedby washesin the transfer buffer. The transfer assembly was set inaBio-Rad Mini gel holder cassette (170-3931)according to manufacturer’s instructions. The transfer time and current settings varied depending on the size oftheprotein of interest. Post transfer, membranes wereseparated from the assembly and kept for blocking intheblocking buffer (0.1 % Tween-20, 5% w/v fat-free skimmed milk in 1X TBS) for 1 h at room temperature with shaking. Next,membranes wereincubated with appropriate dilutions of primary antibodiesin the blocking buffereitherfor 3-4 h at room temperature or overnight at 4°C with gentle shaking. Post incubation,membranes were washed thrice with 1X TBS-T, 10 min each,with constant agitation. After washes, membraneswere incubated with appropriate dilutions of secondary antibodiesconjugated with horseradish peroxidase (HRP) for 1 h at room temperature with gentle shaking. Next, membranes were washed thrice with 1X TBS-T, 10 min each,with constant agitation. To visualize proteins, membranes were removed from TBS-T, and theHRP substrate ECL plus (Amersham Biosciences, RPN2232) was uniformly added on top of the membrane. Chemiluminescent signalswere captured in the western blot imaging system (FluorChemTME system)
    2. For protein extraction, cells were spun down at 4,000 rpm for 5 min and washed with ice-cold water. The cell pellet was resuspended in 250-500 μl of homogenisation buffer which contained50 mM Tris (pH 7.5), 2 mM EDTA, 1 mM phenylmethylsulphonyl fluoride (PMSF) (serine protease inhibitor), 10 mM sodium fluoride (serine/threonine and acid phosphatases inhibitor), 1 mM sodium orthovanadate (Tyrosine and alakaline phosphatases inhibitor) and 1X protease inhibitor cocktail (Sigma, P 8215). The cell suspensison was transferred to a 1.5 ml centrifuge tube and equal amounts of glass beads (0.5 mm size) were added. Cells were lysed mechanically by bead-beatinghomogenizer (MP Biomedicals, FastPrep®-24) atthemaximum speed for 60 seconds, five times each,with intermittent cooling on ice.After lysis, tubes were punctured at the bottom with the helpofasurgical needle, and the lysed cell suspension was collected in a fresh microcentrifuge tubes by putting the punctured tubes on top of the fresh tubes and centrifuging them at 3,000 rpm for 10 min. The supernatant was transferred toafresh microcentrifugetubeandprotein concentrationwasestimated usingtheBCA protein assay kit (Thermo scientific). Protein preparations werestored at -20°C until use