Standard Operating Procedure (SOP) for Bacteroides thetaiotaomicron human marker qpcr Assay

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1 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 1 9/13/2010 Standard Operating Procedure (SOP) for Bacteroides thetaiotaomicron human marker qpcr Assay References: Yampara-Iquise, H., Zheng, G., Jones, J.E. and Carson, C.A. (2008) Use of a Bacteroides thetaiotaomicron-specific Alpha-1-6, mannanase quantitative PCR to detect human faecal pollution in water. J Appl Microbiol 105, Roche Applied Science Light Cycler 480 Operator s manual.

2 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 2 9/13/2010 Recommended Quality Control Procedures: Users must wear gloves at all times and avoid direct hand contact with qpcr reagents to avoid contamination. Use separate designated spaces for reagent preparation and sample addition. Do not move the pipet tips, microtube racks, microtubes, pipettes and other supplies from one space to another. Routinely wipe the hood/bench surfaces with 70% alcohol and UV-disinfect for 15 minutes before and after use. Store reagents in appropriate conditions as per the manufacturer s product manual. 1. Preparation of B. thetaiotaomicron α-1-6, mannanase gene real-time PCR quantification standard solution for the standard curve: Genomic DNA from B. thetaiotaomicron VPI 5482was purchased from American Type Culture Collection, VA, USA (ATCC Number: 29148D-5) and was used for the standardization of qpcr assay Amplification by conventional PCR: a) A section of (~522bp) α-1-6, mannanase gene was amplified from the B. thetaiotaomicron DNA by conventional PCR using the primer set (forward primer 5 GCGGTACACATAACGGG 3 and reverse primer 5 GTTGCCAGTAGATATAAGTCGATT -3 ). b) PCR reaction mixture (total volume of 25µL) was prepared according to the following table. Components of the PCR mix for one reaction: Ingredients Volume /reaction HotStar Taq Master Mix 14.0 µl Forward Primer (10 µm stock) Reverse Primer (10 µm stock) Molecular Grade water 1.0 µl 1.0 µl 6.0 µl DNA template 3.0 µl Total final volume 25.0 µl

3 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 3 9/13/2010 c) PCR thermal cycling program is listed as following. PCR program for amplification of a section of 23srDNA gene. PCR step Cycles Target temperature Hold time (hh:mm:ss) Initial activation 1 95 C 00:10:00 Amplification 35 Denaturation 95 C 00:00:30 Annealing 58 C 00:00:30 Extension 72 C 00:00:60 Final Extension 1 72 C 00:08:00 d) Check the PCR product by agarose gel (1.2%, w/v) electrophoresis (100 V for ~ 1-1.5hrs). A single, discrete band should be observed close to 522 bps maker in the gel Cloning: Clone target alpha-mannanase gene into TOPO vector and transform plasmid vector into TOP10 Competent E. coli cells. Fresh PCR products were cloned into plasmid vector (pcr 2.1 TOPO ) and the plasmid vectors were transformed into TOP10 Competent E. coli cells (One Shot Chemical Transformation) based on TOPO TA Cloning Instruction Manual (Invitrogen, Carlsbad, CA). Things to be done before starting this experiment: Set-up a water bath or heat-block to 42 C. Warm the vial of S.O.C. medium to room temperature. Warm selective plates at 37 C for 30 minutes. Spread 40 μl of 40 mg/ml X-gal on each LB plate and incubate at 37 C until ready for use. (X-gal preparation: 40 mg/ml X-gal in dimethylformamide (DMF)) Thaw on ice 1 vial of One Shot cells for each transformation. a) Prepare a cloning reaction (total volume of 6 µl) based on the table below. Reagent Volume Fresh PCR product 3 µl Salt Solution 1 µl Sterile Water 1 µl TOPO vector 1 µl Final Volume 6 µl b) Mix reaction gently and incubate for 5 minutes at room temperature. c) Place the reaction on ice. d) Add 2 µl of the TOPO Cloning reaction into a vial of One Shot Chemically Competent E. coli cells and mix gently (do not mix by pipetting or vortex).

4 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 4 9/13/2010 e) Incubate on ice for 5 minutes. f) Heat- shock the cells for 30 seconds at 42 C without shaking. g) Immediately transfer the tubes to ice. h) Add 250 μl of room temperature S.O.C. medium. Cap the tube tightly and shake the tube horizontally (200 rpm) at 37 C for 1 hour. i) Spread µl of the transformation on prewarmed selective plates and incubate overnight at 37 C.(The plates should be spread with 40 μl of 40 mg/ml X-gal and incubate at 37 C until ready for use.) j) Pick several (~5) white colonies and grow in 0.5 ml LB amp50 media overnight (or hours) at 37 C. (A single, well-isolated colony is used to inoculate one LB amp50 medium.). k) Add 0.5 ml 40% glycerol, mix thoroughly, and store the E. coli cells (carrying plasmid vectors with target 23srDNA gene) in -20 C freezer Purification of plasmid DNA The plasmid DNA is purified using the QIAGEN Plasmid miniprep. a. Resuspend pelleted bacterial cells in 250 μl Buffer P1 and transfer to a microcentrifuge tube. If LyseBlue reagent has been added to Buffer P1, vigorously shake the buffer bottle to ensure LyseBlue particles are completely dissolved. The bacteria should be resuspended completely by vortexing or pipetting up and down until no cell clumps remain. b. Add 250 μl Buffer P2 and mix thoroughly by inverting the tube 4 6 times. Mix gently by inverting the tube. Do not vortex, as this will result in shearing of genomic DNA. If necessary, continue inverting the tube until the solution becomes viscous and slightly clear. Do not allow the lysis reaction to proceed for more than 5 min. If LyseBlue has been added to Buffer P1 the cell suspension will turn blue after addition of Buffer P2. Mixing should result in a homogeneously colored suspension. If the suspension contains localized colorless regions or if brownish cell clumps are still visible, continue mixing the solution until a homogeneously colored suspension is achieved. c. Add 350 μl Buffer N3 and mix immediately and thoroughly by inverting the tube 4 6 times. To avoid localized precipitation, mix the solution thoroughly, immediately after addition of Buffer N3. Large culture volumes (e.g. 5 ml) may require inverting up to 10 times. The solution should become cloudy. If LyseBlue reagent has been used, the suspension should be mixed until all trace of blue has gone and the suspension is colorless. A homogeneous colorless suspension indicates that the SDS has been effectively precipitated.

5 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 5 9/13/2010 d. Centrifuge for 10 min at 13,000 rpm (~17,900 x g) in a table-top microcentrifuge. A compact white pellet will form. e. Apply the supernatants from step 4 to the QIAprep spin column by decanting or pipetting. f. Centrifuge for s. Discard the flow-through. g. Recommended: Wash the QIAprep spin column by adding 0.5 ml Buffer PB and centrifuging for s. Discard the flow-through. h. Wash QIAprep spin column by adding 0.75 ml Buffer PE and centrifuging for s. i. Discard the flow-through, and centrifuge for an additional 1 min to remove residual wash buffer. Important: Residual wash buffer will not be completely removed unless the flow-through is discarded before this additional centrifugation. Residual ethanol from Buffer PE may inhibit subsequent enzymatic reactions. j. Place the QIAprep column in a clean 1.5 ml microcentrifuge tube. To elute DNA, add 50 μl Buffer EB (10 mm Tris Cl, ph 8.5) or water to the center of each QIAprep spin column, let stand for 1 min, and centrifuge for 1 min Sequencing of PCR product In order to confirm if PCR products are cloned, sequencing of the plasmid is needed. - Preparation of primer and DNA sample for sequence at MSU RTSC The guideline of preparation of primer and DNA sample can be followed according the RTSF website The sequencing center located at S18 Plant Biology Building. - Retrieving sequencing Data Login to the MSU Research Technology Support Center Finch Server. (The lab Username is jbr and password is w5uac0a.r) Click the folders icon at the left side of the screen and then the number under the # Chromats column. Select the sequence data under the Label column. Blast the sequence at NCBI site and analyze the results

6 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 6 9/13/ Quantify purified plasmid DNA Purified plasmid DNA was quantified by spectrophotometer (NanoDrop ND-1000). a) Run 2 µl of molecular grade water as blank. b) Add 2 µl of purified plasmid DNA to the detection tip of NanoDrop ND-1000 to measure the plasmid DNA concentration. c) Repeat measurement 5 times. Ignore the lowest and highest values and average rest of 3 data points. d) Convert the average concentration from ng/µl to copies/reaction. ~4,311 base pair ~660 g/mole/base pair 2,845,260 g/mole. [3,931 bp (pcr 2.1 TOPO plasmid vector) bp (PCR products) = 4,311 bp]. 1 ng ~2,845,260 g/mole mole. (~ mole) (~ copies/mole) copies. Therefore, 1ng/µL plasmid DNA equals to copies/µl (or copies/reaction) Preparation of real-time PCR standard Real time PCR standard can be prepared by diluting in either PCR graded water or negative sample or the elution buffer in which the plasmid DNA was eluted. a) Prepare a standard with molecular grade water Prepare the standard with molecular grade water according to the following table: Components of standard with molecular grade water: Standard Volume of water Volume/Conc of Standard (copies/rxn) (ul) (ul/ copies/rxn) / / / / / / / 10 1 a) Dispense appropriated volume of mixture prepared into each standard tube. Label the tube accordingly.

7 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 7 9/13/2010 b) Mix the newly prepared standard completely and briefly centrifuge to remove drops from the lid or sidewall of the centrifuge tube and mix by pipetting up and down before used for the next serial dilution Quantification of the standard B. thetaiotaomicron α-1-6, mannanase gene by real-time PCR to obtain the standard curve: Ten fold dilutions of standard plasmid were quantified by using following primers and probe, forward primer 5 CATCGTTCGTCAGCAGTAACA3,Reverse primer 5 - CCAAGAAAAAGGGACAGTGG-3 and Probe FAM-ACCTGCTG-BHQ ( Probe ordered through Roche Universal Probe Library; UPL probe # 62). The analysis of this section is further described in section Quantification of B. thetaiotaomicron α-1-6, mannanase gene by real-time PCR from environmental samples and/or standards: 1. Program the LightCycler real-time PCR system (as given below) 2. Wear lab coat, and glove. 3. Disinfect the PCR Preparation Station (i.e., Misonix PCR Prep Station) using 70% EtOH, UV light and/or DNAZap (Ambion). 4. Thaw 5X LightCycler Taqman 480 Probe Master Mix, 10 µm forward primer, 10 µm reverse primer, Magnesium chloride, PCR-grade water, samples and standards. 5. Prepare a super mix for n+2 reactions (n = total samples) in a 1.5 ml centrifuge tube at the PCR Prep Station according to the table. Components of the PCR mix for one reaction in the real-time PCR assay: Ingredients LightCycler Taqman 480 Probe Master Mix BthF primer 1 (10µM stock) Bth R primer 2 (10µM stock) EcuidAProbe 3 (10 µm stock) Volume /reaction 10 µl 0.4 µl 0.4 µl 0.2 µl PCR-grade water 4 µl Total final volume 15 µl

8 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 8 9/13/ Mix the super mix completely and briefly centrifuge to remove drops from lid or sidewall of the centrifuge tube. 7. Dispense 15 µl of the super mix into each LightCycler 96 well plate. 8. Add 5 µl of DNA template from the standards prepared into each assigned well at the sample adding station. 9. Seal the well plate with provided parafilm. Hold the foil by the two outside perforated edges. Separate the foil from the protective coating by pealing the corner of the inner crease and remove the protective layer. Hold the foil by the two edges that still have protective coating still attached. Make sure not to unnecessarily touch the foil with no protective layer results will be affected. Put the foil onto the micro well plate; while making sure that the same side of the foil that was touching the protective coating is the one that will be making contact with the micro well Plate. Square the foil with the micro well plate and place it on to it. Gently push the outside four corners of the foil to make sure it is gently in place. While holding the micro well plate firmly, use the foil applicator to seal each well in place by running one side of it firmly over each well. If a crease forms over the wells get a new foil and start over. Tear off both perforated edges. 10. Bring to the salad spinner and place it in the bottom. Give it 1-2 complete compressions and use the black stop button to stop it spinning 11. Load the 96 well plate into the Roche LightCycler Put reagents, samples, and standard solution back to -20 C freezer. Clean-up the PCR Prep Station and the Sample Addition Station Analyzing the data using Lightcycler Saving the standard curve The standard curve can be saved for future quantification. To save the standard curve, click Standard curve (In Run) and select Save as external. Name the standard curve accordingly. In order to use previously saved standard curve for quantification of unknown samples, each batch of the reaction should contain at least a duplicated standard with the same concentration as one point of the saved standard curve Operation and Programming of LightCycler 480 real-time PCR machine a. Computer login a) Turn on the computer. b) Click the Lightcycler Software icon. Login window will appear. Username is lab and password is rose_lab123. (Log off the computer after turning it on and login again to get the computer started)

9 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 9 9/13/2010 b. PCR reaction programming 1. Click new experiment in the overview menu. 2. The new experiment window should now appear. 3. Set the program conditions (Table 1) and select the ( ) PCR step Cycles Target Temperature Hold Time (hh:mm:ss) Initial Activation 1 95 C 00:15:00 Amplification 50 Denaturation 95 C 00:00:15 Annealing 60 C 00:00:60 Extension 72 C 00:00:05 Cooling 1 40 C 00:00:30 4. Click Start Run 5. Save in appropriate folder 6. Select Subset Editor 7. Choose ABS Quantification 8. Click (+) and name subset appropriately 9. Highlight the appropriate numbers of cells via the mouse and control key then click Apply. 10. Click the Sample Editor 11. Click Toggle View 12. Choose the subset you made prior. 13. Check or uncheck the correct Absorption Wavelength for your samples. (Uncheck the filter) 14. If replicates are present in your micro well plate highlight the replicates and select Make Replicates. 15. Name the samples, give their concentrations if know and give them the distinction of standard (10^6 or 10^5), unknown, negative control, or positive control. 16. Click Experiment to view progress. 17. Upon completion click Analysis and select Abs Quant/ 2 nd Der Max and select the subset and click ( ). 18. Check if lines are appropriate. If not check to see if ABS is incorrect if so change it and see if it has an effect. If yes then calculate then click Calculate. Choose STD external. Select hubactheta std located near the bottom of the list. Recalculate. 19. If creating a standard curve then select the STD Curve button and save as external. 20. Click Report **Must Save For the Report Button to Become Activate** 21. Click Subset that was used 22. Click General tab and X the boxes for Setting, Results, Amp Curve, Standard Curve and STATS also samples if desired. 23. Click Generate 24. Save in folder and print.

10 Asli Aslan, Sangeetha Srinivasan & Joanna Pope Page 10 9/13/ Calculating qpcr Concentrations into qpcr Equivalent Cells/100mL Example Calculation Starting Volume= 1000 ml Pelleted down= 3 ml entire 3 ml used for extraction 200 µl Extracted DNA Volume 1000 ml x _ 5 µl = Assayed Volume 200 µl Copies = Copies/Rxn ) (value from LC 480 e.g * 10^3) ml Assayed Volume Divide by number of copies of target gene/cell (e.g. 1 for α-mannanase) _qpcr eq. cells _ = Copies/Rxn (qpcr concentrations) x mL Assayed Volume

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