protocol for free lipid sop - gwdgkuzyakov/pgz/methods/protocol_free-lipids.pdfprotocol for free...

PROTOCOL FOR Free Lipid SOP

(After optimization by Michaela Dippold)

SOIL SCIENCE DEPARTMENT Rev. 1

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PROTOCOL FOR

FREE LIPID SOP

Kuzyakov Lab

1 30.09.2016 Josh Bostic Michaela Dippold Yakov Kuzyakov

Rev. Date Prep. Modify. Check. Approv.




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Day 1-3

Step 1: Soxhlet Extraction of Bulk Soil

Equipment/Reagents (12 samples)

12 Pre-Milled Dry Soil Samples

Soxhlet Extraction Apparatus (Under hood in Green Lab)

12 Extraction Chambers

12 Condenser/Extraction Chamber Adapter Inserts

12 Glass Sample Thimbles

12, 250mL round-bottom boiling flasks

36 Custom-Cut Glass Filter Papers (See 1.0 below)

Approx 1.5L DCM (HPLC Grade)

Approx 600mL Methanol (HPLC Grade)

1.0: Custom Cut Filter Papers for Sample Thimbles

NOTE: 25mm glass fiber filters DO NOT sufficiently cover the bottom of

soxhlet thimbles. Must make custom filters as follows:

1. Place a 70mm glass fiber filter on a clean countertop. 2. Place a 5mL reactive vial cap that has been sharpened around the edges in one corner of the

filter. 3. Using a clean razor blade, cut the filter paper around the outline of the reactive vial cap. 4. Repeat 2 more times on the filter paper (each 70mm filter paper yields 3 custom-cut filter

papers. 5. Proceed to step 1.1 below. Store unused/Extra Filter Papers wrapped in tin foil for

subsequent soxhlet extractions

1.1: Sample Weighing and Soxhlet Apparatus Assembly

1. Place 2 custom cut filter papers in the bottom of a clean, ashed sample thimble, making sure filter papers are completely flat and covering bottom

2. Weigh 5-6g of Milled, Dry Soil in Thimble using Yellow Sartorius Scale in Red Lab. 3. Record Sample Name, loaded Weight, and Thimble letter/number in lab notebook 4. Place 1 custom cut filter paper on top of soil and lightly press down to seal in sample




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5. Gently lower sample thimble into soxhlet extraction chamber 6. Assemble soxhlet apparatus as follows:

a. Pre-clean condenser units with Acetone prior to beginning (not sure if pervious person cleaned after using).

b. Pour 150mL of 2:1 DCM:MeOH into 250mL boiling flask c. Place boiling flask onto heating apparatus d. Connect soxhlet extraction chamber to boiling flask e. Place condenser adapter insert into extraction chamber and connect extraction

chamber to condenser unit. f. Adjust clamps holding condenser and extraction chamber so that both are secure but

NOT TIGHT (If clamped too tightly, glass may break/crack upon heating). g. Cover the extraction chamber with a blue paper towel to expedite the initiation of

boiling/evaporation process. 7. Repeat the above procedure 11X more times until all samples are loaded.

1.2: Soxhlet Extraction

1. Turn on the flow of water to condensing units with knobs located directly below fume hood (listen for clicking to ensure proper water flow).

2. Turn on heating apparatus and adjust individual heating blocks to 70% for 15 minutes to initiate sample boiling.

NOTE: If evaporation/condensation does not begin after 15 minutes,

blowing on the joint between evaporator and extraction chamber will speed

up process.

3. Once condensation has initiated, lower the heat to 35% and leave for 1 hour 4. After 1 hour, check to make sure the soxhlet extraction is stable and adjust heat as necessary

If condensation slow: Increase heat

If solvent bubbling in boiling flask: Decrease Heat

5. After 12 hours, add 30-50mL DCM to each soxhlet apparatus as necessary to replace evaporated solvent

6. Run soxhlet for a total of 36 hours for soil samples

1.3: Stopping Soxhlet and Solvent Evaporation

1. After 36 hours, turn off water flow to condenser and remove condenser and extraction chamber from soxhlet apparatus.

2. Leave boiling flasks on heating blocks to evaporate solvent from sample (Takes 1-3 hours depending on amount of solvent remaining).

3. Remove sample thimbles from extraction chambers and place on tin foil in hood. Leave overnight to evaporate remaining solvent




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Day 3

Step 2: Liquid-Liquid Separation of Lipid-Extracts


Separating Funnel Stand

8 Glass Separating Funnels

8 Glass Stoppers for Separating Funnels

8 Plastic Stopcocks for Separating Funnels

16, 50mL collection flasks

16, 5mL reactive vials

1.25mL (one GC vial) of Internal Standard 1 (IS1)

200mL Milli-Pure H2O

Saturated NaCL Solution

1M NaOH in MeOH (should we use NaOH in H2O?)

6M HCl

Chloroform

DCM

Methanol

Hexane

2.1: Set-Up and Sample Transfer

1. Clean Separating Funnel Stopcocks with Acetone Prior to Beginning 2. Place Separating Funnels in O-ring stands and insert stopcocks. Test each separating funnel

for leaks by pouring 20mL acetone into funnel and feeling around stopcock for leaks. 3. Add 155uL of Internal Standard 1 to each sample




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4. Transfer sample from round-bottom flasks to separating funnel 3X3 with full glass pipette

(1.5mL) of DCM. 5. Add 20mL of milli-pure water to each separating funnel

In case of weak phase separation, add 500uL of saturated NaCL

2.2: Neutral Fraction (pH 10) Extraction

1. Add 500uL of 1M NaOH in MeOH to each sample. Place stopper on separating funnel and swirl/shake flasks to mix sample and transfer acidic fraction to the aqueous phase.

2. Test pH of sample by touching litmus paper to the separating funnel stoppers. Make sure pH ≥ 10.

3. Add 15mL of chloroform to funnel and close with stopper 4. Shake vigorously by hand for 30” wait 5 minutes for complete phase separation 5. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 6. Add 15mL of chloroform to funnel and close with stopper 7. Transfer closed funnels to shaker and secure with rubber bands around base. 8. Shake 20’ at speed 777. Wait 5 minutes for complete phase separation 9. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 10. Add 15mL of chloroform to funnel and close with stopper 11. Shake vigorously by hand for 30” wait 5 minutes for complete phase separation 12. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 13. Remove 50mL collection flasks and evaporate on Rotivap 14. Transfer sample from 50mL flasks to 5mL reactive vials with 2X Hexane and 1X DCM 15. Dry samples under nitrogen stream and store at -20°C until Step 3 (SPE)

Chloroform Evaporation Conditions

Temp: 39°C

Pressure: 330 mbar

2.3: Acidic Fraction (pH 2) Extraction

1. Add 500uL of 6M HCl to each sample. Close funnel and swirl/shake to mix. 2. Test pH of sample by touching litmus paper to the separating funnel stoppers. Make sure pH

≤ 2. 3. Add 15mL of chloroform to funnel and close with stopper 4. Shake vigorously by hand for 30” wait 5 minutes for complete phase separation 5. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 6. Add 15mL of chloroform to funnel and close with stopper 7. Transfer closed funnels to shaker and secure with rubber bands around base. 8. Shake 20’ at speed 777. Wait 5 minutes for complete phase separation




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9. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 10. Add 15mL of chloroform to funnel and close with stopper 11. Shake vigorously by hand for 30” wait 5 minutes for complete phase separation 12. Open stopcock and SLOWLY drain the lower apolar layer into 50mL collection vial 13. Remove 50mL collection vials and evaporate on Rotivap

Day 4

Step 3: Solid Phase Extraction (SPE) of Neutral Fraction


2 SPE elution Racks

8 metal stopcocks

Glass pipettes

8, 30mL glass SPE columns

8, 6mL SPE glass fiber filter papers

16, 50mL collecting flasks

8, 100mL collecting flasks

24 small cork collection flask holders

Hexane

DCM

Methanol

3.1 SPE Column Set-Up

1. Set Up SPE Elution Rack and Insert Metal Stopcocks. Clean metal stopcocks by rinsing with acetone.

2. Insert 30mL SPE columns into metal stopcocks and close stopcocks. 3. Insert 6mL SPE glass fiber filters into SPE columns. Push down with the blunt end of a long

glass pipette. 4. Draw line 3.5cm from the bottom of the SPE columns with dry erase marker 5. Close stopcock. Transfer 3.5cm of activated silica in hexane to column with a long glass

pipette with tip broken off (prevents silica from clogging pipette) 6. Remove marker line with a Kimwipe soaked in ethanol




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7. Wash any dried silica off the side of the column with hexane. Open stopcock and drain

solvent to waste until solvent is ≈0.5cm above solvent bed. 8. Place 50mL collecting flasks labeled “X Alk” under each SPE column 9. Transfer sample from reactive vials to the solvent bed 3X with hexane. 10. Let sample onto column by slowly opening stopcock and draining until solvent is directly

above silica bed. Close stopcocks.

3.2: Collecting Alkane Fraction

1. Add 30mL Hexane to each SPE column by slowly pouring down sides, making sure not to disturb the silica bed.

2. Open stopcocks and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. Close stopcock.

3. Remove alkane collection flasks and begin evaporating on Rotavap. 4. Using a glass pipette, transfer dried samples from 50mL flasks to reactive vials with 3X

Hexane

3.3: Collecting Aromate Fraction

1. Place 50mL collecting flasks labeled “X Aro” under each SPE column 2. Add 30mL 2:1 Hex:DCM to each SPE column 3. Open stopcocks and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. Close

stopcock 4. Remove aromate collection flasks and begin evaporating on Rotavap. 5. Using a glass pipette, transfer dried samples from 50mL flasks to reactive vials with 3X 2:1

Hex:DCM

3.4: Collecting Alcohol/Ketone Fraction

1. Place 100mL collecting flasks labeled “X Ket” under each SPE column 2. Add 30mL DCM to each SPE column 3. Open stopcocks and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. 4. Add 50mL MeOH to each SPE column 5. Slowly elute (≈1 drip/sec) until solvent is directly above silica bed. OK to let silica bed run dry

at this point. 6. Remove Ketone collection flasks and begin evaporating on Rotavap. 7. Using a glass pipette, transfer dried samples from 100mL flasks to reactive vials with 2X DCM

and 2X MeOH 8. 9. Clean SPE columns by transferring used silica to a plastic bag labeled “Used Silica waste”




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Step 4: Methylation of Acidic Fraction


Heating Block

1000uL pipette with tips

8 clean reactive vials

8 vial caps with Teflon inserts

BF3 in Methanol Solution 14%

Saturated NaCl Solution

Hexane

4.1 Methylation

1. Pre-heat the heating block in the grey lab to 80°C 2. Add 1mL BF3 solution to dry acidic fraction samples and FA/OHFA standards using 1000uL

pipette 3. Close sample vials and roll the vials horizontally a few times to remove dry sample from the

sides. 4. Place samples in the pre-heated heating block (check temperature before starting) and leave

for 15 minutes. 5. Remove samples from heating block and let them cool under the hood for 5 minutes.

4.2 Purification of Methylated acidic fraction

1. Add 0.75mL saturated NaCl to hydrolyze unused BF3 to NaF 2. Add 1mL hexane, close vial, and vortex for 15” 3. Using a glass pipette, remove the upper apolar layer and transfer to labeled reactive vials. 4. Repeat steps 7 & 8 two additional times. 5. Dry methylated samples under N2 stream and store at -20°C until SPE step. 6. Dispose of the remaining polar phase (NaF and BCl3) in proper disposal container.

Day 5




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Step 5: SPE of acidic fraction

5.1 SPE Column Set-Up

1. Set Up SPE Elution Rack and Insert Metal Stopcocks. Clean metal stopcocks by rinsing with acetone.

2. Insert 30mL SPE columns into metal stopcocks and close stopcocks. 3. Insert 6mL SPE glass fiber filters into SPE columns. Push down with the blunt end of a long

glass pipette. 4. Draw line 3.5cm from the bottom of the SPE columns with dry erase marker 5. Close stopcock. Transfer 3.5cm of activated silica in hexane to column with a long glass

pipette with tip broken off (prevents silica from clogging pipette) 6. Remove marker line with a Kimwipe soaked in ethanol 7. Wash any dried silica off the side of the column with hexane. Open stopcock and drain

solvent to waste until solvent is ≈0.5cm above solvent bed. 8. Condition column with 2 column volumes of first elution solvent (2:1 DCM:Hex) 9. Place 50mL collecting flasks labeled “X FA” under each SPE column 10. Transfer sample from reactive vials to the solvent bed 3X with 2:1 DCM:Hex. 11. Let sample onto column by slowly opening stopcock and draining until solvent is directly

above silica bed. Close stopcocks.

5.2: Collecting Fatty Acid Fraction

1. Add 10mL 2:1 DCM: hexane to each SPE column by slowly pouring down sides, making sure not to disturb the silica bed.

2. Open stopcocks and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. 3. Add 20mL DCM and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. Close

Stopcock. 4. Remove FA collection flasks and begin evaporating on Rotavap. 5. Using a glass pipette, transfer dried samples from 50mL flasks to reactive vials with 3X DCM

5.3: Collecting Hydroxy Fatty Acid Fraction

1. Place 50mL collecting flasks labeled “X OHFA” under each SPE column 2. Add 30mL MeOH to each SPE column 3. Open stopcocks and slowly elute (≈1 drip/sec) until solvent is directly above silica bed. Close

stopcock 4. Remove OHFA collection flasks and begin evaporating on Rotavap 5. Using a glass pipette, transfer dried samples from 50mL flasks to reactive vials with 3X MeOH

Day 5-6




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Step 6: Acetylation of Ketones/Alcohols and Hydroxy FA

Step 6.1: Acetylation

1. To dried samples and standards of Ket and OHFA fractions, add: a. 200uL Pyridine b. 200uL of Acetic Anhydride

2. Roll vials horizontally to remove dried sample from side of vial 3. Mix samples for 5 minutes by sonification 4. Leave overnight at room temperature 5. Add 800uL of 4M HCl 6. Add 1mL of hexane and vortex for 15” 7. Transfer the upper apolar layer to labeled reactive vials. 8. Repeat steps 6 & 7 two additional times 9. Purify samples as described in section 6.2

Step 6.2: Purification

1. Place small (3mL) SPE columns on the elution rack and insert a 3mL glass filter in each 2. Fill SPE columns halfway with sodium sulfate anhydrous. 3. Transfer acetylated samples directly onto the columns 4. Collect in clean reactive vials 5. Dry under N2 stream

Day 6

Step 7: Loading Samples/Standards to GC vials

1. Using the EVOL pipette with 50uL syringe, add 15ul of IS2 (FAME 13:0) to each dried sample and standard

2. Using a 250uL pipette, add 185uL of toluene. 3. Roll vials horizontally to remove dried sample from sides of vials 4. Sonificate for 10 minutes. 5. Transfer samples to a 100uL GC-vial insert in 1.5uL GC vials. 6. Cap vial properly 7. Store samples at -20°C until measurement

External Standard Chart:




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volumes (in uL)

Class ES1 ES2 ES3 ES4 ES5

Alkane 30 100 200 300 400

Aromate 50 100 200 300 500

Ketone 50 100 200 300 500

Alcohols 80 200 400 600 800

FA 10 25 75 150 300

OHFA 10 25 75 150 300

Making Internal Standard 1 (All substance stocks 1ug/uL)

Substance List and concentrations

Hexatriacontan in Toluene (alkane): 2500uL

Perylene in MeOH (aromate): 1250uL

Nonadecanol in Toluene (alcohol): 6250uL

2-Pentadecanone in Toluene (ketone): 1875uL

12-hydroxystearic acid in MeOH (OHFA): 2500uL

Nervonic Acid in MeOH (FA): 5000uL

1. Pipette all standards into a 20mL volumetric flask with eVol pipette 2. Fill to 20mL with toluene and sonificate 3. Transfer IS1 mix to ashed 1.5mL GC vials. 4. Store at -20°C until use

Rotivap Evaporation Conditions

Chloroform Temp: 40°C Pressure: 380 mBAR Dichloromethane (DCM) Temp: 40°C Pressure: 700 mBAR Hexane




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Temp: 40°C Pressure: 330 mBAR Methanol Temp: 45°C Pressure: 300 mBAR

protocol for free lipid sop - gwdgkuzyakov/pgz/methods/protocol_free-lipids.pdfprotocol for free...

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