Thomas (1993) says that a researcher must take the familiar, routine, and mundane and make it unfamiliar and new.

Concrete, behavioristi.c descriptions of people's mundane actions may not be amenable to line-by-line coding, particularly when you observed a scene but do not have a sense of its context, its participants, and did not interact with them.

How does the research participant(s) act while involved in this process?

Line-by-line coding works particularly well with detailed data about funda-mental empirical problems or processes whether these data consist of inter-views, observations, documents, or ethnographies and autobiographies.

If you ignore, gloss over, or leap beyond participants' meanings and actions, your grounded theory will likely reflect an outsider's, rather than an insider's view.

starting from the words and actions of your respondents, preserves the fluidity of their experience and gives you new ways of looking at it

Codes are also provisional in the sense that you may reword them to improve the fit. Part of the fit is the degree to which they capture and condense meanings and actions.

Hence, simultaneous data collection and analy~is can help you go further and deeper into the research problem as well as engage in developing categories.

Thus we define what we see as significant in the data and describe what we think is happening.

Coding impels us to make our participants' language problematic to render an analysis of it. Coding should inspire us to examine hidden assumptions in our own use of language as well as that of our participants.

scrutinize your data and define meanings within it Through this active coding, you interact with your data again and again and ask many different ques-tions of them. As a result, coding may take you into unforeseen areas and new research questions.

summary of a wide range of theories and models of onlinemisogyny from the feminist literature, as well as an analy-sis of the works that have targeted the problem of onlinemisogyny from a computational perspective.•The translation of different categories of misogyny, identifiedin feminist theory, into lexicons of hate terms to study theevolution of language within the manosphere.•An in-depth analysis of different manifestations and evolu-tion of misogyny across the Reddit manosphere.•We corroborated existing feminist theories and models aroundthe phenomenon of the manosphere by conducting a large-scale observational analysis.

Full manual analysis is impractical and thus, automatictechniques need to be used.

“I see Posthumanism as a methodology: a conceptual framework that can be applied to the field of graphic design.”

I hope the readerswill take my over-crowded article as an attempt to compose a missingcommunity of posthuman scholars: the essay as assemblage

The reaction mixture contained 0.2 mL of enzyme sample, 0.3 mL of buffer and 0.5 mL of p-nitrophenyl-β-D-glucopyranoside (1.0 mM) prepared in 100 mM buffer as the substrate. The reaction was terminated after 30 min of incubation at 70 °C by adding 2 mL of sodium carbonate-bicarbonate buffer (0.1 M, pH 10.0). The liberation of p-nitrophenol was measured at 400 nm and its yield was determined using a standard curve of p-nitrophenol (1-10 μg mL-1) prepared in sodium carbonate-bicarbonate buffer

β-Glucosidase

The activities ofβ-xylosidase, xylan acetylesterase and arbinofuranosidase were measured using 1 mM p-nitrophenylxylopyranoside, p-nitrophenylacetate and p-nitrophenylarabinofuranoside, respectively prepared in sodium citrate buffer (0.1 M, pH 7.0). One mL of reaction mixture containing 0.2 mL of crude enzyme solution, 0.3 mL of sodium citrate buffer (0.1 M, pH 7.0) and 0.5 mL of substrate was incubated at 80 °C for 30 min. The reaction was terminated by adding 2 mL sodium carbonate-bicarbonate buffer (1.0 M, pH 10.0). The activities were determined using p-nitrophenol standard curve (1-10 μg mL-1) drawn using absorbance values measured in spectrophotometer at 400 nm. One unit of the enzyme is defined as the amount of enzyme that liberates 1μmole of p-nitrophenol mL-1min-1 under assay conditions.

Assays for β-Xylosidase, acetylesterase and arbinofuranosidase

Xylanolytic activity was determined according to Archana and Satyanarayana (1997). The reaction mixture containing 0.5 mL of 1% birchwood xylan in glycine NaOH buffer (0.1 M, pH 9.0) and 0.5 mL of cell free sonicated supernatant was incubated at 80 °C in a water bath for 10 min. After incubation, 1 mL DNSA reagent (Miller, 1959) was added to the reaction mixture and the tubes were incubated in a boiling water bath for 10 min, followed by the addition of 400 μL of 33% w/v sodium potassium tartrate. The absorbance values were recorded at 540 nm in a spectrophotometer (Shimadzu, Japan). The liberated reducing sugars were determined by comparing the absorbance values of these with a standard curve drawn with different concentrations of xylose. One unit (IU) of xylanase is defined as the amount of enzyme required for liberating one μmol of reducing sugar as xylose mL-1 min-1under the assay conditions. Composition of Dinitrosalicylic acid (DNSA) reagent NaOH - 10.0 g Phenol - 2.0 g DNSA - 2.0 g Distilled Water - 1000 mL DNSA reagent was stored in an amber bottle at 4 °C till further use. Sodium sulphite (0.05 % v/v) was added just before the use of the reagent.

Enzyme Assays

A stock solution of xylose (1 mg mL-1) was prepared in distilled water. A dilution series ranging from 100-1000 μg mL-1 was prepared from the stock solution. To 1 mL of solution, 1mL of DNSA was added and kept in a boiling water bath for 10 min and then 400 μL of sodium potassium tartrate solution was added and kept it for cooling. The absorbance was recorded in a spectrophotometer (Shimadzu, UV-VIS) at 540 nm

The clear cell-free supernatants were used as the source of crude recombinant xylanase.

Preparation of standard curve of xylose

Quantitative screening for determination of xylanase in shake flask

Sonicated cells of E. coli having recombinant vector was centrifuged. Supernatant was dispensed into 0.2 % v/v xylan agar plate and incubated for 4 h. The plates were then flooded with Congo red solution (0.2 % w/v) for 30 min and destained with 1M NaCl solution till a clear zone of xylan hydrolysis was visible. The plates were gently shaken on a shaker to accelerate the process of staining/destaining

Qualitative detection of xylanolytic activity by plate assay

DETECTION OF XYLANASE ACTIVITY

Overnight grown cultures of E. coli DH5α, E. coli BL21 (DE3), E. coli XL1blue cells with and without constructs were preserved in 80 % v/v glycerol

MAINTENANCE OF THE RECOMBINANT STRAIN

Metagenomic library obtained from various extracted DNA was screened by replica plating method on 0.3 % w/v RBB xylan containing LB-amp plates. The cells were allowed to grow for overnight at 37 °C and thereafter incubated at 4 °C till the appearance of zone of hydrolysis. A total of 36,400 clones from various environmental samples were screened.

SCREENING OF THE TRANSFORMANTS FOR XYLANASE ACTIVITY

Transformation of calcium-competent cells was carried out by the procedure detailed below: •The competent bacterial cells were thawed briefly and 200 μL of cells was mixed rapidly with plasmid DNA (10-50 ng) in fresh, sterile microcentrifuge tubes and maintained on ice for 30 min. A negative control with competent cells only (no added DNA) was also included. •Cell membranes were disrupted by subjecting cells to heat-pulse (42 °C) for 90 sec. •After heat shock, cells were incubated on ice for 5 min. •Cells were then mixed with 1 mL LB medium and incubated with shaking at 37 °C for 1 h. •For blue/white screening 40 μL of X-gal solution (20 mg mL-1 in dimethylformamide) and 4 μL of the IPTG (200 mg mL-1) was spread on LB-ampicillin (LB-amp) plates with a sterile glass rod. The plate was allowed to dry for 1h at 37 °C prior to spreading of bacterial cells. •Bacterial cells (100-200 μL) were spread and the plate was incubated at 37 °C for overnight. •White colonies were picked from the plates and suspended into LB-amp broth and cultivated to OD600=0.5

Transformation procedure

2 mL of an overnight culture of E. coli cells was inoculated into 100 mL LB medium and incubated with vigorous shaking at 30 °C until A600 of 0.8 was reached. •Cells were collected in 50 mL plastic (Falcon) tubes, cooled for 15 min on ice and centrifuged in a pre-cooled centrifuge (4,000 rpm for 10 min at 4 °C). •The pellet was suspended in 20 mL of ice-cold 50 mM CaCl2-15% glycerol solution, maintained on ice for 15 min and centrifuged again at 4,000 rpm for 10 min at 4 °C. •Pellet was resuspended in 2 mL of ice-cold 50 mM CaCl2-15 % glycerol solution, kept on ice for 30 min and aliquoted in 400 μL in microcentrifuge tubes. These were stored at -80 °C until required.

Preparation of calcium-competent cells

Preparation of electrocompetent cells (E. coli cells) A protocol was employed. The procedure was carried out in cold under sterile conditions as follows: •A single colony of E. coli DH10B/ DH5α/XL1blue was inoculated in 20 mL of LB medium and grown overnight at 30 °C. •500 mL LB medium was inoculated with 5mL of this overnight grown culture of the E. coli and incubated with vigorous shaking (250 rpm) at 30 °C until an A600of 0.5 - 0.8 was achieved. •The cells were chilled in ice for 10-15 min and transferred to prechilled Sorvall® centrifuge tubes and sedimented at 4,000 rpm for 20 min at 4 °C. •The supernatant was decanted and cells were resuspended in 500 mL of sterile ice-cold water, mixed well and centrifuged as described above. •The washing of the cells described above was repeated with 250 mL of sterile ice-cold water, following which cells were washed with 40 mL of ice-cold 10 % (v/v) glycerol and centrifuged at 4,000 rpm for 10 min. •The glycerol solution was decanted and the cell volume was recorded. The cells were resuspended in an equal volume of ice-cold 10 % glycerol. •Cells were then dispensed in 40 μL volumes and stored at -80 °C until required.

Electrotransformation

BACTERIAL TRANSFORMATION

PurifiedDNA fragments of size 2-8 kb were ligated to the treated vector using a 1:3::vector :insert ratio in a volume of 10 μL. The total amount of DNA was about 0.5 μg. Vector and insert DNA was heated to 45 °C for 10 min and the immediately chilled on ice for 5 min prior to addition of ligase and buffer. T4 DNA ligase (NEB, England) was added to a final concentration of 0.125 UμL-1 and reactions were incubated at 16 °C for overnight in a ligation chamber. Reaction mixture incubated under same condition without addition of the enzyme was used as control. A ligation reaction was also set up under condition with linear plasmid DNA containing the

Ligation of insert DNA with dephosphorylated vector

In order to minimize self ligation of vector during cloning experiments, the digested DNA was subsequently treated with calf intestinal phosphatase (CIP) [NEB, UK]. The reaction conditions and amount of CIP were optimized and varied from (0.06-1) unit/picomole DNA termini. The dephosphorylation reaction was carried out in 50 μL reaction as follows. Reaction mixture containing no restriction enzyme was treated as control. Reaction was incubated for 1 h at 37 °C and stopped by heat inactivation at 65 °C for 20 min. 2.5.5. Composition of restriction mixture (50 μL) Linearized Plasmid DNA X μL (1 μg) CIP 1 μL (0.06-1 U μL-1) Reaction buffer (10X) 5.0 μL Distilled water Y μL Total volume 50 μL Linearized and dephosphorylated plasmids from each reaction were purified from low melting agarose gel using gel extraction method according to the manufacturer’s protocol (Qiagen gel extraction kit, Germany). 100 ng DNA from each reaction was then ligated in15 μL reaction volume containing 1.5 μL of 10X ligation buffer (NEB, England) and 0.2 μL of T4 DNA ligase to check the efficiency of self ligation after dephosphoryaltion. The ligation mixture was incubated at 16 °C for overnight and transformed into E. coli DH5αcompetent cells.

Dephosphorylation of the restricted plasmid

The vector isolated as above was digested with BamHI to generate the cohesive ends. The reaction was performed in 1.5 mL Eppendorf tubes as described below. Composition of restriction mixture (100 μL) Plasmid DNA X μL (20 μg) Bam HI 8 μL (10 U μL-1) NEB buffer 4 10.0 μL BSA (100X) 1 μL MQ water Y μL The reaction mixture was incubated at 37 °C for 3 h. The digestion was stopped by heat inactivation at 65 °C for 20 min. The digestion of plasmid was checked using 1.2 % (w/v) agarose gel electrophoresis for linearization of the plasmid. The digested plasmid was purified from low melting agarose gel using gel extraction method according to the manufacturer’s protocol (Qiagen gel extraction kit, Germany).

Restriction digestion of plasmid DNA

Two hundred μL of alkaline-SDS solution was added to the above suspension, mixed by inverting the tubes up and down 3 times and incubated for 5 min at room temperature. ƒTo the above mixture, 250 μL of 3 M Na-acetate (pH 4.8) was added, mixed by inverting the tubes up and down 3 times, and centrifuged at 12,000 x g for 10 min. ƒThe supernatant was collected in another micro centrifuge tube (MCT), 200 μL of phenol:chloroform solution was added, inverted two times and centrifuged at 12, 000 x g for 8 min at room temperature. ƒThe aqueous phase was transferred to new tubes and 500 μL of chilled (-20 °C) ethanol (96 %) was added. ƒThe tubes were centrifuged at 13,000 x g for 25 min at 4 °C, supernatant discarded and pellet dried for 15 min at room temperature. ƒThe pellet was washed with 500 μL of chilled 70 % (v/v) ethanol and centrifuged at 13, 000 rpm for 4 min at 4 °C. ƒThe pellet was dried at room temperature and dissolved in 50 μL of 1X TE buffer (pH 8.0) containing RNase and stored at -20 °C till further use.

The cells of E. coli DH10B having p18GFP vector were cultivated for overnight at 37 °C in LB medium containing ampicillin (100 μg mL-1). ƒThe E. coli culture having p18 GFP vector (~1.5 mL) was taken in Eppendorf tubes and centrifuged at 10, 000 x g for 5 min. ƒThe pellet was homogenized by vortex mixing in 100 μL of homogenizing solution

Plasmid isolation from miniprep method

The metagenomic DNA extracted from above defined protocol was digested with Sau3A1 at conditions optimized to generate maximum fragment in the size range of 2-6 kb. Different concentration (0.05 to 1 unit) of enzyme was used to optimize the digestion of 1 μg of DNA. Reactions were carried out in a final volume of 30 μl each in an Eppendorf of 1.5 mL. Reaction mixture (1 μg DNA having 3 μL NEB buffer 3 and 0.3 μL of 10X BSA) were kept at 37 °C for 10 min and stopped by heat inactivation at 80 °C for 20 min. Different digested reactions were checked for the desired fragments using 0.8 % (w/v) agarose gel electrophoresis. After optimization of DNA fragments for the appropriate size, a large scale digestion was carried out and the fragments (2-8 kb) were purified from low melting agarose gel using gel extraction method according to the manufacturer’s protocol (Qiagen gel extraction kit, Germany)

Insert DNA preparation

CONSTRUCTION OF METAGENOMIC LIBRARY

An attempt was made to study the effect of storage of DNA extracts on DNA yield and purity. The DNA extracts were centrifuged and the supernatants were dispensed into 2.0 mL Eppendorf tubes and stored at -20 oC for a month. DNA precipitation and its quantification were carried out at a week intervals.

Effect of storage on soil/sediment DNA extracts

Attempts have been made to amplify the signature sequences of bacterial, archaeal and fungal specific regions by using respective sets of primers shown in Table2.2. The reactions were carried out in 50 μL reaction mixtures in a Thermal Cycler (Bio-Rad, USA) using respective primers (Table 2.2). The PCR conditions were optimized as follows: for Bacterial 16S rDNA, initial denaturation of 3 min at 94 oC followed by 30 cycles of 30 sec at 93 oC, 60 sec at 55 oC and 90 sec at 72 oC; Archaeal 16S rDNA, 5 min at 95 oC, 35 cycles of 50 sec at 94 oC, 60 sec at 62 oC and 60 sec at 72 oC; fungal specific ITS regions, 3 min at 95 °C, 30 cycles of 60 sec at 94 °C, 56 °C at 45 sec and 50 sec at 72 °C. Final extension time was 7 min at 72 °C in all PCR runs. Amplifications were visualized on 1.2 % w/v agarose gels

PCR amplification of microbial population

Purity of the DNA extracted from various environmental samples was confirmed by subjecting the extracted DNA to restriction digestion. DNA was digested with Sau3AI (New England Biolabs). One μg of metagenomic DNA in 20 μL reaction mixture was treated with 0.5 U of Sau3AI and incubated at 37 °Cfor 10 min. The reaction was terminated at 80 °C for 20 min and the digested DNA was fractionated on 1.2 % (w/v) agarose gel.

Restriction digestion

VALIDATION OF METAGENOME OBTAINED BY THE PROTOCOL DEVELOPED IN THIS INVESTIGATION

The isolated DNA was diluted (1:100) with MQ. The concentration (mg mL-1) of the DNA [N] was determined spectrophotometrically by recording absorbance at 260 nm (A260) as: A260 = ε 260[N]where ε 260 is the extinction coefficient of DNA (50 for ds DNA) [N] = concentration (mg mL-1) of DNA The concentration of ds DNA [N] was calculated as [DNA] (mg mL-1) = A260/ε 260 [DNA] (μg mL-1) = A260 × 50 × dilution factor Purity of DNA was checked by measuring absorbance at 260 and 280 nm and calculating the A260/A280 ratio (Sambrook et al., 1989). A DNA sample was considered pure when A260/A280 ranged between 1.8-1.9. An A260/A280 < 1.7 indicated contamination of the DNA preparation with protein or aromatic substances such as phenol, while an A260/A230 < 2.0 indicated possible contamination of high molecular weight polyphenolic compounds like humic substances.

Determination of DNA quantity and purity

as well as commercial methods (MN kit, Germany; Mo-Bio kit, CA, USA; Zymo soil DNA kit, CA, USA) according to the manufacturer’s protocols and compared in terms of DNA yield and purity.

The soil DNA from Pantnagar and Lonar soil samples were also extracted by various manual (Desai and Madamwar, 2007; Agarwal et al., 2001; Yamamoto et al., 1998

Alternatively metagenomic DNA was extracted from the alkaline soil samples by using different commercial kits (UltraClean™, PowerSoil™ [Mo Bio Laboratories Inc., Carlsbad, CA, USA], Nucleospin kit [Macherey-Nagal, Germany] and Zymo soil DNA isolation kit [CA, USA]). The DNA was finally suspended in 100 μL of sterile Milli Q water for further analysis.

Commercial kits

Comparison of yield and purity of crude DNA

Soil (1 gm) was suspended with 0.4 gm (w/w) polyactivated charcoal (Datta and Madamwar, 2006) and 20 μL proteinase K (10 mg mL-1) in 2 mL of modified extraction buffer [N,N,N,N cetyltrimethylammonium bromide (CTAB) 1% w/v, polyvinylpolypyrrolidone (PVPP) 2% w/v, 1.5 M NaCl, 100mM EDTA, 0.1 M TE buffer (pH 8.0), 0.1M sodium phosphate buffer (pH 8.0) and 100 μL RNaseA] [Zhou et al., 1996] in 20 mL centrifuge tubes to homogenize the sample and incubated at 37 °C for 15 min in an incubator shaker at 200 rpm. Subsequently, 200 μL of 10% SDS was added to the homogenate and kept at 60 °C for 2 h with intermittent shaking. DNA was precipitated by adding 0.5 V PEG 8000 (30 % in 1.6 M NaCl) and left at room temperature for an hour (Yeates et al., 1998). The precipitated DNA was collected by centrifugation at 8000 x g at 4 °C. The supernatant was discarded and pellet was dissolved in 1 mL of TE buffer (pH 8.0) and then100 μL of 5 M potassium acetate (pH 4.5) was added and incubated at 4 °C for 15 min. The supernatant was collected after centrifugation at 8000 x g and treated with equal volumes of phenol: chloroform (1:1) followed by chloroform: isoamylalcohol (24:1) at 8000 x g for 15 min

PROTOCOL FOR OPTIMIZATION OF HUMIC ACID-FREE DNA FROM ALKALINE SOILS

Various strains of Escherchia coli (DH5α, XL1Blue, DH10B) were used as hosts for the propagation of recombinant vectors. In addition, Bacillus subtilis was used as a host for the expression of xylanase gene from the recombinant vector pWHMxyl. Different vectors used in this investigation are listed in

BACTERIAL STRAINS

Soil, sediment, effluent, and water samples have been collected from various hot and alkaline regions of India and Japan in sterile polyethylene bags/bottles. The samples were transported to the laboratory and preserved at 4 °C. Temperature and pH of the samples was recorded.

COLLECTION OF SAMPLES

The CLD-J domain shares ~51 % similarity with the CDPK from Arabidopsis thaliana AtCPK-l. The homology model of CLD-JD was determined using Swiss Model from EMBL. The template model used was CLD-JD of AtCPK-1, which was crystallized as a dimer. The J -domain helices from the two monomers were swapped with each other in this structure (Chandran et aI., 2006). Therefore, the initial homology model generated for the complementary CLD-J domain for PfCDPK4 was also a dimer. To understand the interaction of this helix (Gln358_ Lys371) with CLP of the monomer, this helix was rotated and translated keeping residues 372-375 as the flexible linker region and superimposed on to the helix from the other monomer, which resulted in the initial model for the CLD-J domain monomer. Initially, these flexible linker residues (372-375) were locally minimized using COOT (Emsley and Cowtan, 2004), and the overall structure was refined with slow cooling using annealing of CNS (Brunger et aI., 1998) to remove all the short contacts. Finally, the model quality was checked with the Pro check software (Laskowski et aI., 1996). The homology model was generated with the help of Dr. S. Gaurinath, JNU

Homology Modeling

DAPI 01 ector Labs, USA), and stained parasites were visualized using Zeiss Axioimager fluorescence microscope and the images were processed using Axio Vision software

Thin blood smears of parasite cultures were fixed with chilled methanol for 2 min. After air drying, washing with PBS and permeabilization was done with 0.05 % saponin in 3% BSA/PBS for 15 min, followed by blocking with 3% BSA made in PBS for Ih. Subsequent incubations with primary antibodies were performed for 2h at room temperature or at 4°C overnight. The smears were washed 3x5 times with PBS. The slides were then incubated with appropriate secondary antibodies (labeled either with fluorescein isothiocyanate (FITC) or Texas Red) for 1 hour at I room temperature. The slides were washed again with PBS and air dried in the dark. Smears were mounted in glycerol containing mounting media that contained

mmunofluorescence Assay

Gametocyte rich parasite lysate was prepared using lysis buffer containing phosphatase inhibitors (20IlM sodium fluoride, 20llM ~-glycerophosphate, and IOOIlM sodium vanadate). For some experiments, 2mM calcium or 2 mM EGTA was added to the lysis buffer. IOOllg of lysate protein was incubated with PfCDPK4 anti-sera (1:100 ratio) for 12 h at 4°C on an end-to-end shaker. Subsequently, 50 III of protein A+G-Sepharose (Amersham Biosciences) was added to the antibody-protein complex and incubated on an end-to-end shaker for 2 h. The beads were washed with phosphate-buffer saline three times at 4°C and were resuspended in kinase assay buffer that contained phosphatase inhibitors.

mmunoprecipitation of PfCDPK4 from parasite lysates

temperature for 2h. The nitrocellulose membrane was washed extensively with PBST and developed using chemiluminescence substrate from Pierce (USA).

The proteins separated by SDS-PAGE were transferred from the gel to· nitrocellulose membrane using a blotting apparatus (Bio-Rad, USA). In brief, after removal of the stacking gel, the resolving gel was placed over nitrocellulose membrane and sandwiched with Whatman 3 mm filter paper in a cassette. The cassette was submerged in transfer buffer and transfer was carried out at 150 rnA for 3h at 4°C. Following the transfer, the membrane was carefully removed from the blotting apparatus and blocked with 3% non-fat dry milk protein for Ih. The membrane was washed thrice with PBST and incubated overnight with the primary antibody at 4°C. Following incubation, the membrane· was washed thrice with PBST and incubated with appropriate HRP-labeled secondary antibody at room

Western Blot

A 96-well microplate was coated overnight at 4°C with ovalbumin conjugated peptide in 100 mM carbonate buffer, pH 9.5 (2 /J-g/well). The plate was washed 3 times with PBST and blocked with PBS containing 2% BSA (200/J-l/well) at 37°C for 1 h. Serum samples (diluted in PBS) were added in duplicates (50 (/J-lIwell) at different dilutions (1: 1 00, 1: 1000, 1: 10,000) and the plate was incubated at 37°C for 1 h. The plate was washed and incubated with HRP-conjugated appropriate antibody (1: 1 0,000 dilution in PBS containing 2% BSA) at 37°C for 1 h. The plate was washed thoroughly with PBST and freshly prepared TMB substrate (100/J-lIwell) was added and the reaction was stopped with 2 N H2S04 (50 (/J-l/well) and the absorbance at 450 nm was recorded in an ELISA reader

ELISA

A synthetic peptide (KMMTSKDNLNIDIPS) based on the PfCDPK4 sequence was custom synthesized (Peptron Inc.) and conjugated to keyhole limpet hemocyanin via an additional N terminus cysteine residue. It was used to raise polyclonal antisera against PfCDPK4 in rabbit. First immunization was performed using 1 00 ~g of peptide diluted in PBS and mixed 1: 1 v/v with Complete Freund's Adjuvant (CF A). Subsequently, three booster doses of 50 ~g each were given on the 14th, 28t\ 42nd day post first immunization. Blood was collected from animais on 7th, 21 S\ 35th, 49th day. Antibody titers were checked by ELISA using recombinant proteins or ovalbumin conjugated peptides as an antigen. In all cases, pre immune sera from the same rabbit were used as control

Generation of anti-PfCDPK4 antisera

Parasite cultures were distributed in six well plates (2 ml per well) and pharmacological inhibitors were added at desired concentration. Plates were placed in small gas chambers, gassed and immediately returned to 37°C incubator. The lysates were prepared after ~30 min of the addition of inhibitors

Inhibitor Treatment of gametocyte

suspension through a 26 gauge needle. Lysates were cleared by centrifugation at 14,000 g for 30 min at 4°C and supernatant was used for protein estimation using BCA protein estimation kit (Pierce)

P. Jalciparum infected erythrocytes were lysed by the addition of 0.05 % (w/v) saponin to release parasites, followed by a 30 minute incubation on ice. To remove debris and lysed RBCs were washed with cold PBS followed by centrifugation at 8000g. The lysis buffer containing 10 mM Tris pH 7.5, 100 mM NaCl, 5 mM EDTA, 1% Triton X-100, and Ix complete protease inhibitor cocktail (Roche Applied Science) was added to the parasite pellet and homogenized by passing the

Preparation of Parasite Cell Lysate

containing 50 mM Tris, pH 7.5, 10 mM magnesium chloride, 1 mM dithiothreitol, and 100 11M p_32p] ATP (6000 Cilmmol) using 6 Ilg of Myelin Basic Protein. Kinase assays were also performed using "syntide-2" a small peptide substrate (PLARTLSV AGLPGKK) custom synthesized by Peptron, South Korea, and has been used as a substrate for plant CDPKs and CaMKs (Harmon et al., 1994; Hashimoto and Soderling, 1987; Yoo and Harmon, 1996). Reactions were performed in the presence of 2 mM calcium chloride or 2 mM EGTA (0 mM Ca2+) for 40 min at 30°C. When MBP was used as the substrate, reactions were stopped by boiling the assay mix for 5 min in Lammeli's buffer followed by SDS-PAGE. Phosphate incorporation was adjudged by autoradiography of SDS-PAGE gels. When Syntide-2 was used as substrate, reactions were stopped by spotting the reaction mix on P81 phosphocellulose paper (Millipore). The paper strips were air dried followed by washing with 75 mM ortho-phosphoric acid. Phosphate incorporation was assessed by scintillation counting of the P81 paper. In PfCDPK4 inhibition assays, peptide inhibitors were preincubated with proteins in a kinase assay buffer at 25°C for 30-60 min prior to the addition of substrate and ATP

The catalytic activity of recombinant PfCDPK4 (and its mutants), as well as irnrnunoprecipitated PfCDPK4 from parasite lysate, was assayed in a buffer

ssay of Protein Kinase Activity

The protein samples were resolved by SDS PAGE using the Laernrnli buffer system (Laernrnli, 1970). The protein sample was denatured by boiling at 100°C for 10 min in Laernrnli's buffer (List I). Resolving gel (10%) was prepared in a minigel (Bio-Rad, USA) system alongwith 3% stacking gel and the electrophoresis was carried out at 120 volts for 125 min. The gel was stained with 0.25% Coomassie blue R staining solution for Ih followed by destaining with successive washes of de staining solution. Staining was avoided when. gel was used for irnrnunoblotting. Details of reagents used for SDS-PAGE are given in List 1.

SDS PAGE

Protein concentrations were detennined using BCA protein estimation kit (Pierce, .. USA). The assay was perfonned according to the instructions provided by the manufacturer. Various dilutions of the sample or BSA were made in appropriate buffer and 200 J.ll of supplied reagent mix (1 :50 ratio) was added to each well in a 96 well plate. The plate was incubated at 37°C for 1 h and the absorbance was measured at 540 nrn.

Protein Estimation

Tris, pH 7.4, 1 mM dithiothreitol, and 10% glycerol. Protein concentration w~s detennined by densitometry analysis of Commassie stained gels. Protein samples were stored at -70°C until further use

To facilitate the expression of recombinant GST-CDPK4 or its mutants, the desired regions of enzyme were PCR amplified using pGEMT-PfCDPK4 as template and PCR primers which possessed overhangs for XhoI and SmaI restriction enzymes (see List II). Often, the PCR products were cloned in TA cloning vector pGE¥T-I easy. Clones in pGEMT-easy vectors were digested with appropriate restriction enzymes to release the inserts. The released inserts were cloned in expression vector pGEX4T-l to facilitate the expression of recombinant proteins. In some cases, the PCR products were digested directly with restriction enzymes and ligated into expression vectors. The plasmid DNA for expression was used to transform E. coli BL21-RIL (Stratagene) strain for the expression of GST-PfCDPK4 and its mutants. Protein expression was induced by overnight incubation of cells with O.lmM IPTG at 18-20°e. Subsequently, cell pellets were suspended in ice cold lysis buffer, contaiJ;1ing 50 mM Tris, pH 7.4, 2 mM EDTA, 1 mM dithiothreitol, 1% TritonX-100, and protease inhibitors (lmM phenylmethylsulfonyl fluoride, 10~g/ml leupeptin, 1 O~g/ml pepstatin) and sonication was performed for 6 cycles of one minute each. The resulting cell debris was removed by centrifugation at 20,000g for 40 min at 4°C. Fusion proteins from the cell lysates were affinity-purified using glutathione-sepharose resin (Arnersham). Briefly, after the protein binding, the resin was washed with lysis buffer, and bound proteins were eluted with 50 mM Tris, pH 8.0 with 10 mM glutathione. Finally, purified proteins were dialyzed against 50 mM

xpression and Purification of Recombinant GST (Glutath ion e-S-Transferase) fusion PfCDPK4 and its mutant

All site-directed mutagenesis studies were performed usmg the QuickChange mutagenesis kit (Stratagene) following the manufacturer's instructions. It is a PCR based method for introducing point mutations, replace amino acids and delete or insert single or multiple amino acids into desired plasmid constructs. Primers containing mutations were designed and PCRs were performed using "wildtype" construct as template. The PCR product was' subjected to digestion with DpnI endonuclease, which is specific for methylated DNA. Following DpnJ digestion, the parental DNA template gets cleaved and DNA containing desired,mutation is selected. The residual mutant nicked DNA was transformed in E. coli DH5a competent cells and the resulting plasmids were isolated and sequenced to confirm incorporation of the desired mutations.

ite directed mutagenesi

incubated on ice for 5 min, buffer N3 (350 J.!l) was added to the mixture and the tube was iriverted 4-6 times until mix appeared cloudy. Cell debris was removed by centrifugation at 12000 x g for 10 min and the supernatant was applied to QIAprep spin columns. Columns were centrifuged at 12000 x g for 1 miri and the flow through was discarded and columns were washed using 750 J.!l of 70% ethanol and centrifuged, at 12000 x g for 1 min. Additional centrifugation was performed to remove the residual ethanol. The columns were placed in a 1.5 ml microfuge tube and DNA was eluted with autoclaved water or 1 mM Tris-HCI (PH 8.0).

Plasmid DNA was extracted using commercially available kit (Qiagen, Germany) as per manufacturer's instructions. For a miniprep, bacterial cell pellet from 5ml freshly grown culture were resuspended in 250 III buffer PI containing RNaseA in a microfuge tube, followed by lysis in 250 III of buffer P2. After the tube was

Plasmid DNA Isolation

5 III of the ligation mix was added to competent cells and mixed gently and the mix was kept on ice for 30 min before giving a heat shock at 42°C for 1 min. The· mixture was incubated on ice for 2 min and 900 III of LB broth was added to each tube. The cells were recovered by centrifugation at 250 rpm at 37°C for 1 h and were plated on LB agar plates containing the appropriate antibiotic(s) and incubated overnight at 37°C

Transformation in E. coli

The ligation reaction consisted of 10 ng of vector, appropriate amount of insert (insert:vector ratio :: 3: 1), 1 x ligation buffer and 1 U of T 4 DNA ligase (NEB, England). The total volume was made up to 10 III with autoclaved water. The ligation reaction mixture was incubated at 16°C for 12 hrs

Ligation

cycles at 94°C for 30 s, 45°C for 30 s, 68°C for 2 min and final extension at 72°C for 10 min (see table 3.1). PCR products were cloned in pGEM-T easy vector (Promega) and the sequence for the cloned PfCDPK4 gene was obtained by automated DNA sequencing

The PCR reaction was carried out usmg Hi-fi Platinum Taq polymerase (Invitrogen) and primers PfCDPK4_F and PfCDPK4_R (see list II) with the following cycling parameters: 94°C for 2 min initial denaturation followed by 3

To obtain PfCDPK4 gene sequence, BLAST search was done usmg either i TgCDPK1 or the published sequence of other CDPKs in the P. Jalciparum genome sequence. An ORF on chromosome 7 exhibited significant sequence homology with other PfCDPKs. Subsequently, PlasmoDB annotation appeared in the public domain and the gene sequence PF07 _0072 matched with the PfCDPK4 sequence! identified by us. For PCR amplification, primers were designed on the basis of' nucleotide sequence of PFb7 _0072. Total RNA from asynchronous P. Jalciparum, cultures was isolated using RNA easy Kit (Qiagen, Germany) and was used to' synthesize cDNA for reverse transcription (RT). Both complimentary and genomic DNA were used as template.

Molecular Cloning of PfCDPK4

Parasites from synchronized cultures were harvested at different time points of growth to obtain ring, trophozoite and schizont stage parasites. RNA was isolated from these stages by using RNAeasy kit (Qiagen) following manufacturer's protocol. The concentration of total RNA was determined by measuring the absorbance at 260 nm. Purity of nucleic acid preparations were determined by calculating OD26onm / OD28onm ratio, a value of near ~ 1.6-1.8 was taken as a standard of purity. To get stage specific cDNA from RNA, reverse transcription was performed using RT-PCR kit (Invitrogen) that contained random hexamers. Subsequently, the gene of interest was amplified using gene specific primers

Isolation of the parasite RNA

or DNA isolationJrom P. Jalciparum, genomic DNA kit from Qiagen (Germany) was used. Isolation was done following manufacturer's instructions. Briefly, infected erythrocytes (5 ml at 10% parasitemia) were centrifuged at 3,000 g for 2 min. The cells were washed once in cold PBS and resuspended in 1 ml. Following which, 10 ilL of 5% saponin (final concentration 0.05%) was added and' mixed gently. After lysis, the mix was immediately centrifuged at 6,000 g for' 5min. Further steps were, carried out according to the manufacturer's instructions to isolate genomic DNA. DNA was quantified by measuring absorbance at 260 nm I using a UV -spectrophotometer

Genomic DNA Isolation from Parasite Culture

Enzymatic assays using acyl-peptidyl substrates were set up as follows: 100-120 llmoles of purified ~PL/RNRP protein, 200 l!M valeryl-FT AA-CoA/ valery 1-FT AAlaninal and 2 mM NADPH were incubated at 30°C for 2 hrs. The protein was precipitated with acetonitrile and the reaction was loaded on C 18 RP HPLC column (250 x 4.6 mm, 5l!, phenomenex). The products could be resolved using following gradient: 0 to 48% B in 25 min, 48% B in 40 min and 70% B in 50 min (A-water with 0.1% TF A and B-acetonitrile with 0.1% TF A) at a flow rate 0.6 ml/min. The elution profile was monitored at 220 nm. The identity of peaks obtained was confirmed by TOF-MS and tandem mass spectrometric analysis using ESI-MS (API QSTAR Pulsar i MS/MS, Applied Biosystems).

The enzymatic assays were performed as described for wild type ~Pl. in chapter 2. The standard reaction mixture contained 100 J.lM fatty acyl-CoA (30 J.lM [1-14C] fatty acyl-CoA (55 mCi/mmole,ARC) and 70 J.lM of unlabeled fatty acyl CoA), 2 mM NADPH and 10-20 nmoles protein for l-2 hrs. Lauroyl aldehyde [ l-14C] was obtained enzymatically from [ l-14C] lauric acid (55mCi/mmole,ARC) using the FadD9 protein, and extracted from TLC by using ethyl acetate. Assays were set up using a total of 100 J.lM ('4C labeled + unlabeled) of lauroyl aldehyde in the presence of 2 mM NADPH and 10-20 nmoles protein for 1-2 hrs. The products were extracted twice in 300 J.ll of hexanes and resolved on silica gel 60 F2s4 TLC plates (Merck) using hexanes:ethyl acetate (80:20, v/v) solvent system. The radiolabeled product was detected by using phosphorimager (Fuji BAS500)

nzymatic assays and product characterization

sodium sulphate, filtered and concentrated. The product was reconstituted in methanol and desalted using LH-20 sephadex column. The identity of the aldehyde was confirmed by TOF-MS and tandem mass spectrometric analysis using ESI-MS (API QST AR Pulsar i MSIMS, Applied Biosystems). Purification of peptide was performed using RP-HPLC. The aldehyde could be resolved from other impurities (including traces of alcohol, valeryl-FTAAlaninol) on Cl8 RP-HPLC column (7.8 x 300 mm, 125A, Waters) using a gradient of 0-48% B in 20 mins, 48% B in 40 mins and 90%B in 50 mins (A: water with 0.1% TF A and B: acetonitrile with 0.1% TF A) using a flow rate of 2 mllmin. The elution profile was monitored at 220 nm and the identity of the aldehyde was confirmed by mass spectrometric analysis

The aldehyde valery I-L-Phe-L-Thr-L-Ala-L-Alaninal (valery!-FT AAlaninal) was synthesized by Fmoc-solid phase solid phase chemistry using the Weinreb AM resin (Novabiochem, 0.63 mM/g) and automated peptide synthesizer (Advanced Chemtech. USA). Fmoc protecting groups of amino acids were removed by 20% piperidine in double distilled dimethyl formamide (DMF). A fourfold excess of respective amino acids were preactivated using HoBt (2 equivalents) in DMF and the coupling was catalyzed by diisopropylcarbodiimide (DIPCDI, 2 equivalents). After synthesis resin was dried with dichloromethane/DCM (3 X) and MeOH (3 X). The Thr side chain protecting group (tertiary butyl) was removed by treatment with 60:40, TF A: DCM, twice. The filtrates were discarded and resin was washed with DCM (3 X) and MeOH (3 X). The dried resin was suspended in tetrahydrofuran (3 ml) in a glass reaction flask (25 ml) under nitrogen, swelled with gentle stirring for 1 h, and then cooled to 0 °C. Cleavage of the peptide aldehyde from the resin was performed by adding lithium aluminium hydride (Aldrich. 2 M equivalents dissolved in THF) drop wise for 30 min at 0°C with constant stirring. The reaction was quenched with careful addition of KHS04 (saturated solution) and stirred until the solution reached room temperature. The resin was then filtered off and washed with DCM (3 X) and MeOH (3 X). The filtrate was treated with sodium potassium tartrate (saturated solution) and organic layer was extracted. This organic layer was dried over

Clzemical synthesis and purification of aldehyde valeryl-FTA-Aianina

proteins of interest were pooled and 1 mM TCEP was added. The protein of interest was collected and stored at -80°C for further use after adding 1 mM TCEP.

The mutant proteins were expressed and purified analogous to wild type RaPt protein. Mutant clones pAC36, pAC50 and pAC38 were transformed in BL21 strain of E. coli. Analogous to the wild type RGPL protein the cells harbouring the mutant expression plasmids were cultured at 37°C to an O.D6oonm of 0.6 and uninduced at 30°C for 6-8 hrs. After harvesting, the cells were resuspended in lysis buffer (1 00 mM phosphate pH: 7 .0, I 0% glycerol) and disrupted using french press at 1100 psi pressure. Cell debris was removed by centrifugation at 50,000 g for 40 min at 4°C. 0. 75 ml L.1 of Ni2+ -NT A slurry was added to the supernatant and incubated at 4°C for 1 hr. This suspension was loaded onto a column working under gravity flow. The resin was washed with wash buffer (100 mM phosphate pH: 7.0, 10% glycerol and 5 mM imidazole) till all unbound proteins were removed. The protein was eluted using elution buffers containing increasing concentration of imidazole. Fractions containing the

Expression and purification of RcPL mutant proteins

~PL mutants were generated using QuickChange site-directed mutagenesis kit (Stratagene). Mutagenesis reactions were performed in accordance with the manufacturer's protocol using pAC28 (wild type ~PL gene fragment cloned in pET28c, section 2.3.3.1) as template. The details of oligonucleotides used for generating the mutant clones are given in table 3.1. Translationally silent restriction sites were engineered in the oligonucleotides whenever possible, in order to facilitate preliminary screening of mutant clones. Mutant clones were screened by restriction endonuclease analysis and confirmed by automated DNA sequencing

Site directed mutagenesis to generate RGPL mutant clones

Methods

Optiphot fluorescence microscope, E600W fluorescence microscope and T2000E Confocal microscope Cl were from Nikon (Tokyo, Japan). Multitemp III water bath and EPS 500/400 power supply were obtained from Amersham Pharmacia Biotech (Uppsala, Sweden). Gyratory water bath shaker was purchased from New Brunswick Scientific Co., Inc (Edison, NJ). Centrivac and Biofuge table top centrifuge were from Heraeus (Allerod, Denmark). f.!-Quant microplate reader was from Bio-tek Instruments Inc. (Winooski, VT). Protean II polyacrylamide gel system and Mini Trans blot system were from Bio-Rad Laboratories (Hercules, CA). Submarine DNA electrophoresis system was procured fro Bangalore Genei (Bangalore, India). Laminar flow hoods were purchased from Kartos Ltd. (New Delhi, India). Eppendorf 581 OR centrifuge was purchased from Eppendorf (Hamburg, Germany). LS50B flourimeter was from Perkin Elmer Biosystems (Norwalk, CT). Fluostar Optima fluorimeter was from BMG labtech (Offenburg, Germany) BD-LSR flow-cytometer was from Bectinson Dickinson Biosciences (San Jose, CA). Peltier Thermal Cycler-200 was purchased from MJ research (Waltham, MA). Doc-It Gel Documentation system was procured from UVP Bio Imaging System Incorporation (Upland, CA)

Instrumentation

Densitometric measurements for quantitation of signals on immunoblots or ethidium bromide stained agarose gels . were performed using a UVP Gel Documentation instrument, and the acquired data was analyzed on Lab Works image analysis and acquisition software (UVP, v.4.0.0.8). Data from at least 3 experiments were quantitated to arrive at the average value of the signal. All measurements were normalized to internal loading controls. To determine statistical significance, the data was analyzed by Student's T test and the values were expressed as mean±SEM. The values were considered to be significantly different at p<0.05

Densitometry and statistics

DNA was sequenced by the di-deoxy method (10) at the DNA sequencing facility of Department of Biochemistry, University of Delhi, South Campus, New Delhi, India

DNA sequencing

he DNA fragments eluted from the agarose gel were cloned into pGEM-TEasy vector which allows efficient sequencing using the sequencing primers for T7 and SP6 promoters. 3 )lL of eluted DNA (1 )lg/)lL) was ligated with 1 )lL ofpGEM-TEasy vector in the presence of 1 )lL of T4 DNA ligase in a 10 )lL reaction volume. The reaction was allowed to proceed at 4 oc for 16 h following which 8 )lL of the ligation mix was used to transform DH5-a strain of E.coli following standard protocols (9). The transformation mix was spread onto LB-agar plates containing appropriate ampicillin (100 )lg/mL) and the blue-white selection reagent (40 )lLiplate) (Sigma chemical company). The plate was incubated at 37°C for 12 h following which the white colonies were picked up for screening for presence of the gene of interest.

Sub-cloning ofPCR products into pGEM-TEasy vector

To elute DNA from agarose gel, the samples were loaded on a gel (1-1.8%) cast with low melting point agarose (LMP agarose ). The samples were resolved and visualized under UV transilluminator, and the band of interest was excised quickly using a scalpel blade. The volume of gel slice was quantitated by weighing and the DNA eluted using MinElute Gel Extraction kit (Qiagen) as per manufacturer's protocol. Briefly, the gel was solubilized by incubating it with buffer QG at 50°C for 10 min. The solubilized gel was loaded onto binding columns and centrifuged at 12,000 x g for 1 min. The flow-through was discarded and the column was washed once with buffer PE containing ethanol. The DNA bound to the column was eluted using the elution buffer provided with the kit, or alternatively with nuclease-free water. The concentration of the obtained DNA was estimated by measuring the absorbance at 260 nm (A26o) and using the following formula: DNA concentration= A260 X 50 X dilution factor.

Elution of DNA from agarose gel

DNA fragments were resolved on 1-2% agarose gel containing 0.5 )lg/mL ethidium bromide in Tris-Acetate-EDTA (TAE) buffer (40 mM Tris-acetate, 2 mM EDT A, pH 8.1 ). The samples were mixed with 6X loading dye containing bromophenol blue, and the samples were resolved by applying a voltage of -5-7 V/cm. The resolved DNA fragments were visualized under ultraviolet illumination and the relative band size was determined by comparison against a DNA ladder with bands of known sizes. When required, images were acquired using a UVP Gel Documentation system.

Agarose gel electrophoresis

72°C for 45 s - 1 min. A final extension at 68-72°C for 10 min was performed. Relative expression of specific genes in cells subjected to different treatments was determined by semi-quantitative PCR. The optimal number of cycles required for achieving a linear amplification of serially diluted template was determined, which was then used with other samples to quantify the expression of specific genes. The PCR products were resolved on 1-2% agarose gel containing ethidium bromide and visualized under ultraviolet illumination. The specific primers used are shown in Figure 3.1.

Polymerase chain reaction (PCR) was used to amplify specific nucleotide sequences from eDNA derived from human macrophages. The reaction consisted of Gene Forward primer Reverse primer ER-a 51-GTGGGAATGATGAAAGGTGG-31 51-TCCAGAGACTTCAGGGTGCT-31 51-TGAAAAGGAAGGTT AGTGGGAACC-ER-~ 51-TGGTCAGGGACATCATCATGG-31 31 Bcl-2 51-GTGGAGGAGCTCTTCAGGGA-31 51-AGGCACCCAGGGTGATGCCA-3' Mcl-1 51-CGGCAGTCGCTGGAGATTAT-31 51-GTGGTGGTGGTTGGTTA-31 51-TGGAGTGTCCTTTCTGGTCAACAG-Bfl-1 51-AGCTCAAGACTTTGCTCTCCACC-31 31 iN OS 51-GGCCTCGCTCTGGAAAGA-3 I 51-TCCATGCAGACAACCTT-31 51-CTCCTT AATGTCACGCACGATTTC-Actin 51-GTGGGGCGCCCCAGGCACCA-3 I 31 Figure 3.1. The table shows the forward and reverse pnmers designed agamst specific genes used for amplifying products using PCR. an initial denaturation at 94°C for 4 min, followed by 20-30 cycles of denaturation at 94°C for 30 s, annealing at primer specific temperature for 30 s, and extension at 68

Polymerase Chain Reaction

First strand synthesis of mRNA into eDNA was performed using First strand eDNA synthesis kit from Invitrogen following manufacturer's protocol. Briefly, 4 jlg of total RNA was denatured at 65°C for 5 min in the presence of Oligo dT 16 and dNTPs and incubated at 42°C for another 2 min with DTT, MgCb, and RNaseOUT in 10 X reverse transcription buffer. 1 IlL/reaction of the Superscript Reverse Transcriptase enzyme was added to the denatured RNA and incubated at 42°C for 50 min. The enzyme was denatured by heating at 70°C for 15 min. The reaction was completed by a quick high-speed centrifugation and the complementary RNA strand degraded by incubating with RNaseH for 20 min at 37°C. The preparation was stored at -70°C.

First strand synthesis by reverse transcription

X dilution factor X 40) of the obtained RNA was determined by measuring the absorbance at 260 nm (A26o) and 280 nm (A2so).

Total RNA was isolated from cells usmg TRizol reagent following the manufacturer's protocol. Briefly, 2x106 cells were harvested by non-enzymatic cell dissociation buffer and washed once with PBS. The cell pellet was lysed with 1 mL ice-cold TRizol reagent. The lysate was centrifuged at 12,000 x g for 10 min at 4°C to pellet down cellular debris, polysaccharides, and high molecular weight DNA. The supernatant was gently decanted into a fresh microcentrifuge tube and 200 J.tL of chloroform /mL of TRizol was added and the tube was shaken vigorously for 15 s. The mixture was incubated at room temperature for 2-3 min before centrifugation at 12,000 x g for 15 min at 4°C. This resulted in the separation of the mixture into a lower organic phase and an upper aqueous phase. The aqueous phase containing the RNA was gently aspirated and transferred into a fresh microcentrifuge tube and 500 JlL of isopropanol /mL of TRizol reagent was added to precipitate the RNA. The mixture was centrifuged at 12,000 x g for 10 min at 4°C to isolate the RNA as a pellet. The supernatant was discarded and the pellet was washed once with 70% ethanol, centrifuged and the pellet was air-dried and re-dissolved in appropriate quantity of nuclease-free water. The purity (A26o/A2so > 1.8) and concentration (A260

Total RNA isolation

Molecular biology techniques

The cutaneous lesion developed in the L. major infected footpad and tissue from the corresponding region of normal footpad was harvested for histopathological examination. The tissue was fixed in 4% formaldehyde for 24 h following which the tissue was dehydrated by incubating it with ascending concentrations of alcohol (50%, 70%, and 100% ethanol for 1 h each). Subsequently, tissue clearing was performed by incubating with xylene for 1 h following which paraffin embedding was performed. The embedded tissue was cut into multiple sections of 5 J.tm thickness using a microtome. The paraffin sections were then coated on slides and deparaffinization was carried out by treating with xylene. Subsequently, hematoxylin-eosin staining was performed and the slides were visualized under a light microscope.

Histopathological examination of cutaneous leishmaniasis lesion

5x105 L.major promastigotes were cultured in 5 mL modified DMEM supplemented with 10% FCS. At the end of 5 days of culture, the stationary phase promastigotes were harvested and resuspended in Hanks balanced salt solution at a cell density of 4x107/mL. The cell suspension was aspirated into a 1 mL syringe and 50 J.!L was injected into the footpad of mice. The mice were returned to the cage and fed ab-limitum. The onset and progression of cutaneous lesion was monitored at 2 weekly intervals by observing an increase in the thickness of the footpad

L.major infection in mouse footpad

The mice were returned to a cage and were kept under a 1 OOW bulb light source to prevent hypothermia. Care was taken to ensure that the eyes are kept covered. The respiratory rate and heart rate were monitored till the mice regained complete consciousness. They were fed ab-limitum post-operatively. Metronidazole (20 mg/kg) was added to the drinking water and the mice were fed this medicated water for 5 days post-operatively. On the th post-operative day, the health of the wound was observed and the surgical clips were removed from the skin

ost-operative care

Sham surgery was performed on mice as described above except that the ovary and tubes after being delivered from the incision site were pushed back into the peritoneum in an intact state

Sham surgery:

released from the para-ovarian pad of fat as well as from the peritoneal reflections while care was taken to avoid injury to the ovarian vessels. A ligature was tied around the distal end of the fallopian tube including the ovarian vessels following which the ovary was excised. Hemostasis was secured before the stump of the tube was pushed back into the peritoneal cavity. The peritoneum was closed by continuous sutures using 2-0 silk. The same protocol was followed to perform oophorectomy on the contralateral side. The muscular layer and skin were closed together using surgical clips

The anesthetized mice were operated under strict aseptic conditions inside a laminar flow hood. The mouse was placed over layers of sterile tissue paper and the skin overlying the dorsal flanks was sterilized by wiping with 70% ethanol. The flank was palpated gently to identify the kidney, and an incision(~ 5 mm) was made using a pair of scissors on the overlying skin which penetrated the skin, sub-cutaneous tissue and the muscle layer with the parietal peritoneum being exposed and intact. The para-ovarian pad of fat was identified through the intact peritoneum and a small incision was made on the peritoneum overlying it. The ovarian tissue along with the fallopian tube was mobilized and delivered through the incision site. The ovary was

Bilateral oophorectomy

Hair from the skin overlying the left and right dorsal flanks were removed using electrically operated razor. The skin overlying the abdomen was sterilized by wiping with 70% ethanol. Ketamine (1 00 mg/kg) and xylocaine (2%) (20 mg/kg) were mixed and administered intraperitoneally. The mice were returned to the cage and the onset of anesthetic effect was monitored. The mice were considered to be in surgical anesthesia when there was loss of palpebral reflex, righting reflex, and toe pinch reflex. Respiratory rate and heart rate were monitored continuously.

General anesthesia:

Bilateral oophorectomy, the surgical removal of both the ovaries, was performed in mice to simulate a condition of estrogen depletion. All procedures in mice were performed after obtaining approval from the Institutional Animal Ethics Committee (National Institute of Immunology, New Delhi). Female BALB/c mice were used in the study

Bilateral oophorectomy and sham surgery in mice

Animal experiments

resh complete medium was added and the plates were transferred to 37°C for further incubation. The percentage infection was monitored at appropriate time intervals post-infection by staining the cells with Syto Green 11 nucleic acid dye and the parasite nuclei were visualized by fluorescence microscopy

Human THP-1 macrophages were plated at a density of 2X105 cells per well in a 24 well plate and appropriate treatments were given. The stationary phase L.major promastigotes were opsonized with 1% human AB serum in PBS for 5 min at 37°C following which one wash was given with phenol-red free RPMI-1640 medium. The L.major promastigotes were added to the macrophage culture at a macrophage: parasite ratio of 1:10 or 1:50 and incubated for 6 hat 37°C following which the unbound parasites were removed by giving 3 washes with warm RPMI-1640 medium

Leishmania major infection of human macrophages in vitro

nzyme-linked immunosorbent assay (ELISA) was performed to detect cytokine secretion from human THP-1 macrophages upon activation with LPS. The ELISAs were performed according to manufacturer's protocol. Briefly, THP-1 macrophages were subjected to various treatments and after appropriate time interval the cell culture supernatants were harvested. The capture antibodies for the individual cytokines were diluted 1:250 in coating buffer (0.1 M Sodium carbonate, pH 9.5) and 100 flL was ali quoted into each well of a 96 well ELISA plate (BD biosciences ). The plates were incubated at 4°C for 16 h following which three washes with 0.05% PBS-Tween-20 were given. Blocking was performed using 200 flL of assay diluent (PBS with 10% FCS) per well for 1 h at room temperature following which 1 00 flL of appropriately diluted standards and samples were added and incubated for 2 h at room temperature. A total of 5 washes with 0.05% PBS-Tween-20 were given and the plates were subsequently incubated with 100 flL of detection antibody and streptavidin-HRP for 1 h at room temperature following which 5 washes were given. 100 flL of tetramethylbenzidine (TMB) substrate was aliquoted into each well and incubated for 15 min at room temperature in dark following which 50 flL of stop solution (2N H2S04) was added to terminate the reaction. The absorbance was read at 450 nm and the cytokine levels in the samples were derived based on the OD45o values obtained with standards of known concentration

Cytokine ELISA

bacteria. The cells were washed once with ice-cold PBS and the uptake of labeled bacteria was analyzed by flow-cytometry

The phagocytic ability of macrophages was determined by monitoring the uptake of Bioparticles® Alexa fluor 488 labeled dead E. coli (Molecular Probes, Eugene, OR). 2X105 THP-1 macrophages were plated per well in a 24 well plate. Alexa fluor 488 labeled dead E. coli particles were opsonized with an opsonizing reagent obtained from Molecular Probes. These opsonizing reagents are derived from purified rabbit polyclonal IgG antibodies that are specific for E.coli. These opsonized bioparticles® were transferred to the macrophage culture at an multiplicity of infection (MOl) of 1:10, i.e., 10 bacteria per macrophage. The plates were briefly centrifuged at 250 x g to allow the bacteria to settle at the bottom of the plate and were then transferred to an incubator maintained at 37°C and 5% C02 in air for 1 h. The culture medium was aspirated to remove excess unbound bacteria and the cells were washed 3x with ice-cold PBS. To eliminate fluorescence from non-phagocytosed bacteria adhering to the macrophage membrane, 0.25 mg/mL Trypan blue was added and incubated for 10 min to quench the fluorescence of extracellula

Measurement of phagocytic ability of macrophages

Nitric oxide (NO) generation within the macrophage was detected using the fluorescent NO-sensitive probe DAF-FM diacetate (7). THP-1 macrophages were harvested and resuspended in serum and phenol-red free RPMI-1640 medium and incubated at room temperature for 30 min in the presence of 1 llM DAF-FM diacetate dye. The cells were washed once with fresh medium to remove the excess probe and kinetic fluorescent measurements were performed on a spectrofluorimeter (BMG Fluostar Optima) at an excitation of 480 nm and emission of 520 nm. Time kinetic measurements were performed after appropriate treatment and the values were represented as arbitrary fluorescence units with the comparisons being made against the fluorescence of the control cells. SNAP (S-nitroso-N-acetylpenicillamine), a photoactivatable nitric oxide donor (8) was used as positive control in the assay.

Measurement of intracellular nitric oxide (NO) generation

were represented as arbitrary fluorescence units and comparisons were made against the untrea!ed control samples. Exogenous addition of hydrogen peroxide to cells was used as a positive control for the assay

he generation of reactive oxygen species in macrophages was detected by fluorimetry using the fluorescent dye CM-H2DCFDA, which can detect hydrogen peroxide, hydroxyl radical, peroxyl radical, and peroxynitrite anion (5, 6). To perform the assay, THP-1 macrophages were washed and resuspended in serum and phenol-red free RPMI-1640 medium and incubated at room temperature for 30 min in the presence of CM-H2DCFDA at a final concentration of 1 JiM. Subsequently the cells were washed once with fresh media to remove the excess probe and fluorescence measurements were commenced on a spectrofluorimeter (BMG Fluostar Optima) at an excitation of 480 nm and an emission of 520 nm. Appropriate treatments were initiated and time-kinetic measurements were carried out and the values obtained

Detection of intracellular reactive oxygen species generation

Intracellular Na + measurement was performed using the fluorescent Na + indicator Sodium Green TM tetracetate. THP-1 macrophages were resuspended in phenol-red free RPMI-1640 medium and incubated with Sodium Green™ at a final concentration of 1 JiM for 20 min at room temperature. The cells were washed once with fresh serum-free media to remove excess probe following which kinetic fluorescent measurements were commenced in a spectrofluorimeter (BMG Fluostar Optima) at an excitation of 480 nm and emission of 520 nm. In situ calibration to determine the dissociation constant (Kct) of the dye at 3 7°C was accomplished by using the indicator dye in solutions of precisely known free Na+ concentration in the presence of the pore forming antibiotic gramicidin (10 J,tM). Intracellular Na+ was calculated using the following formula: where, Kct of the dye is 5.7 mM at 37°C, F is the fluorescence of the experimental sample, Fmin is the fluorescence in the absence of Na+ and Fmax is the fluorescence under saturating concentrations ofNa+ in the presence of gramicidin (10 J.i.M)

Assay for intracellular Na +measuremen

at the acidic and basic endpoints of the titrations. Na+ free and HC03-free buffer were prepared as described by Khaled et al.

Intracellular pH measurement was performed using the long-wavelength fluorescent pH indicator carboxy SNARF-1 AM. THP-1 macrophages were resuspended in serum-free and phenol-red free RPMI-1640 medium (106 cells/mL) and incubated at room temperature for 15 min with SNARF-1 AM at a final concentration of 1 f.!M. The cells were washed once in fresh serum-free media and incubated for 20 min for complete de-esterification of intracellular acetoxymethyl esters. In situ calibration ofSNARF-1 AM was performed to determine the pKa of the dye at 3 7°C by using the ionophore Nigericin (1 0 f.!M), which maintains the intracellular pH the same as that of the controlled extracellular medium in a buffer containing high-K+. Appropriate groups were subjected to different treatments and fluorescence measurements were commenced in a spectrofluorimeter (Perkin Elmer, Waltham, MA, USA) followed by kinetic analysis. The pH was calculated from the fluorescence measurements using the following formula: where pKa of carboxy SNARF-1 AM is 7.5 at 37 °C. R is the ratio of fluorescence intensities (F) measured at two emission wavelengths, 580 nm (AI) and 640 nm (A.2), with fixed excitation at 514 nm. The subscripts A and B represent the limiting values

Measurement of intracellular pH

esterification of the dye. Basal fluorescence was measured in a fluorimeter (BMG Fluostar Optima spectrofluorimeter) at an excitation of 480 nm and an emission of 520 nm. Appropriate treatments were initiated and kinetic fluorescence measurements were performed with the temperature being maintained at 3 7°C. At the end of each experiment, a calibration was performed to convert the fluorescence values into absolute calcium concentration using the following formula: where, Kt is the dissociation constant of Ca2+ -Fluo3-AM complex (325 nM), and F represents the fluorescence intensity of cells, Fmax represents the maximum fluorescence (obtained by treating cells with 1 f.!M Ca2+ ionophore A234187 in the presence of 4 mM CaCh), and Fmin corresponds to the minimum fluorescence (obtained by treating cells with 4 mM EGTA)

Cytosolic free Ca2+ was measured using the fluorescent Ca2+ indicator Fluo3-AM. THP-1 macrophages were harvested and resuspended in Kreb's buffer (118 mM NaCl, 25 mM NaHC03, 4.8 mM KCl, 1.2 mM KH2P04, 1.2 mM MgS04, 11 mM glucose, 1.5 mM CaCh.2H20). Fluo3-AM was added at a final concentration of 0.5 J.LM alongwith 1 J.LM Pluronic acid F-127 to aid in dispersal of the dye. The cells were subjected to constant mixing by end-to-end rotation and incubated with the dye for 20 min at room temperature following which the cells were pelleted and resuspended in fresh Kreb' s buffer and incubated for further 15 min to allow complete de-

Intracellular free Ca2+ assay

Sub-cellular fractionation of THP-1 macrophages was performed after lysis with hypotonic buffer. THP-1 macrophages after appropriate treatment were allowed to swell for 10 min in hypotonic buffer (1 0 mM NaCl, 1.5 mM MgCh, 10 mM Tris-HCl, pH 7 .5) followed by homogenization with 50 strokes using a Dounce homogenizer. More than 90% cellular lysis was ensured by visualizing under a light microscope, and immediately after lysis, the mitochondrial membranes were stabilized by addition of 2.5x mitochondrial stabilization buffer (525 mM mannitol, 175 mM sucrose, 12.5 mM Tris-HCl, 2.5 mM EDTA, pH 7.5) to a final concentration of 1x. The homogenate was centrifuged at 1300 x g for 15 min to isolate the nuclear fraction. The post-nuclear fraction was further centrifuged at 17,000 x g for 15 min in an ultracentrifuge (Beckman Optima XL-1 OOK ultracentrifuge) to isolate the mitochondria. The post-mitochondrial supernatant was centrifuged at 100,000 x g for 1 h to obtain the membranous fraction as a pellet and the supernatant obtained was the cytosol. The homogeneity of the obtained fractions was determined by probing for fraction specific proteins by Western blotting

Sub-cellular fractionation

antibody at an appropriate dilution. The immunoreactivity was detected by enhanced chemiluminescence using an ECL detection kit (Amersham Biosciences) and were recorded on X-ray films after appropriate exposure and development. It is important to note that the blots for probing phosphorylated proteins were performed using 1% BSA as blocking agent instead ofblotto

Whole cell extracts were prepared by treating cells with lysis buffer (0.125M Tris, 4% SDS, 20% glycerol, and 10% ~-mercaptoethanol), and protein estimation was performed using CB-X protein assay kit as per manufacturer's protocol. Lysates were resolved on 12% SDS-PAGE gel, following which Western transfer was performed onto nitrocellular membranes using a BioRad Western transfer apparatus. The blots were incubated with 5% blotto (non-fat dry skimmed milk) in 0.05% PBS-Tween 20 for 1 h to block non-specific binding sites following which they were incubated for 1 h with primary antibody at an appropriate dilution prepared in 1% blotto in 0.05% PBS-Tween-20. The blots were washed 3x with 0.05% PBS-Tween-20 at 5 min intervals following which they were incubated for 1 h with secondary

SDS-PAGE and Western blot

THP-1 macrophages and human peripheral blood monocyte derived macrophages were transfected with SMARTpool Bcl-2 siRNA (15 pmol), or ER-a siRNA (100 pmol), or ER-~ siRNA (100 pmol), or with negative control siRNA (15 pmol or 100 pmol) using TranspassR2 transfection reagent. Prior to transfection, the cells were depleted of serum by washing 2x with serum-free media. The transfection complex was prepared by diluting 0.5 J!L of transfection reagent A and 1.0 J!L of transfection reagent B to 400 J!L of serum-free media and siRNA's were added to the mix at an appropriate concentration and incubated for 20 min at room temperature. The formed transfection complexes were transferred gently using a large bore pipette tip to 105 cells/well grown in 24 well plates and incubated for 6 h, following which fresh complete medium was added. Transfection efficiency was estimated by observing Cy3-fluorescence of the negative control siRNA with a Nikon TE2000E fluorescence microscope using a tetramethyl rhodamine filter (530-580 nm). For all transfections, target protein knockdown was assessed 24 h after transfection by probing extracts oftransfected cells on Western blots using appropriate antibodies

siRNA transfection

cold PBS followed by incubation with fluorophore labeled secondary antibody at appropriate dilution for 30 min at 4°C. The fluorescence was then visualized under a fluorescence microscope or analyzed by flow cytometry

Immunostaining in Live cells: Immunostaining on live cells was performed by harvesting and resuspending cells in ice-cold PBS. The cells were then incubated with an appropriate dilution of the primary antibody for 1 h at 4 °C following which two washes were given with ice-

Immunostaining in fixed cells: The cells were fixed with 4% formaldehyde for 20 min, following which two washes were given with ice-cold PBS. Permeabilization and blocking were performed simultaneously by incubating the formaldehyde fixed cells in PBS containing 0.1% saponin and 3% normal goat serum for 30 min. The cells were washed once with ice-cold PBS. The permeabilized cells were incubated with the primary antibody at an appropriate dilution for 1 h at room temperature following which three washes with ice-cold PBS was given. These cells were then incubated with fluorophore conjugated secondary antibody (IgG) for 1 hat room temperature following which three washes with ice-cold PBS were given. The nuclei were stained with Hoechst 33342 at a concentration of 1 Jlg/mL for 2 min at room temperature. The staining was then visualized under a Nikon TE2000E fluorescence microscope using appropriate filter blocks. Image acquisition was carried out using a high-resolution Retiga Exi camera (Q-imaging, Surrey, BC, Canada) and subsequent image analysis was performed on Image-Pro Plus software v5.5 (Media Cybernetics, Silver Spring, MD). Alternatively, the fluorescence staining was detected by flow-cytometry (BD-LSR, Beckton Dickinson, NJ, USA) using an air-cooled argon ion laser (488 nm) at appropriate florescence channels. Subsequent data analysis was performed on WinMdi software (Microsoft, v 2.9)

Immunocytochemistry

700 mM NaCl, 12.5 mM CaCh, pH 7.4). 5 J.!L of Annexin-V conjugated to Alexa fluor 488 and 1 J.!L of working solution of PI (100 Jlg/mL) were added to the 100 J.!L cell suspension. Cells were incubated for 15 min at room temperature. Following this, 400 J.!L of IX Annexin binding buffer was added to dilute the sample. The samples were placed on ice. The fluorescence was measured by flow cytometry in FL 1 and FL2 channels for Annexin-V-Alexa fluor 488 and PI fluorescence respectively.

The Vybrant apoptosis assay kit was used to perform Annexin-V/PI staining as described previously (3). The assay is based on the principle that apoptotic cells show loss of membrane asymmetry by exposing phosphatidylserine on the outer surface of the plasma membrane for which Annexin-V, a phosphlipid binding protein, shows high affinity. Hence, Annexin-V conjugated to Alexa fluor 488 binds to phosphatidylserine exposed on apoptotic cells, while propidium iodide binds to nucleic acids of all non-viable cells including necrotic and apoptotic cells. Thus, flow-cytometric analysis of Annexin-V /PI stained cells reveals distinct cellular populations, with the viable cells displaying little or no fluorescence; the early apoptotic cells show green fluorescence of Annexin-V conjugated to Alexa fluor 488; the late apoptotic cells display both green and red fluorescence, while necrotic cells show red fluorescence. The cells after appropriate treatment were harvested by centrifugation at 250 x g for 5 min and were given two washes with ice-cold 1X PBS following which they were resuspended in 100 J!L of ice-cold 1X Annexin binding buffer (50 mM HEPES,