Merge branch 'saschulz-main' into main

docs/_Experimental-Procedure-Standards-SOPs/04-DNA-and-RNA-kits-by-sample.md

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+---
+title: DNA and RNA kits by sample
+category: Experimental-Procedure-Standards-SOPs
+layout: default
+docs_css: markdown
+---
+
+
+# Nucleic Acid extraction kits
+
+## DNA extraction
+
+- Sponges - QIAamp® DNA Micro kit (QIAGEN)1
+- Sponges –DNeasy® PowerSoil® Pro Kit (QIAGEN)1
+- Human blood viruses - QIAAMP Ultra Sens Virus Kit (Qiagen)2
+- Water samples - PowerSoil® DNA Isolation Kit (MoBio)3
+- Saliva - QIAamp® DNA Mini kit (Qiagen)4
+- Crushed fruit fly larvae - DNeasy PowerLyzer PowerSoil Kit-100 (Qiagen)5
+- Frog skin swab – Prepman Ultra (ThermoFisher)6
+- Skin swabs - PureLink® Genomic DNA Mini Kit (Life Technologies)7
+- Skin swaps - Kaneka Easy DNA Extraction Kit version 2 (Kaneka Corp)8
+- Oral swaps - QIAamp DNA mini kit (Qiagen)9
+- Skin swaps - QIAamp blood and tissue DNA extraction kit (Qiagen)9
+- Oyster haemolymph - Qiagen DNeasy Blood and Tissue Kit (Qiagen)10
+- Molluscs - E.Z.N.A. Mollusc DNA (Omega Biotek)11
+- Melted ice cave water - MoBio PowerWater DNA Isolation kit (MoBio)12
+- BAL, oral rinse, tongue scraping, bronchoscope flush - DNeasy Blood and Tissue kit (Qiagen)13
+- Lake sediment - PrestoTM Soil DNA Extraction Kit14
+- Oral Swabs - Maxwell RSC PureFood Pathogen Kit (Promega)15
+- Plant DNA - Mo Bio PowerSoil kit (Qiagen)16
+- Gastric juice - DNeasy® PowerSoil Pro kit (Qiagen)17
+- Saliva - DNeasy® PowerSoil Pro kit (Qiagen)18
+- Bacterial DNA - DNeasy PowerSoil Kit (QIAGEN)19
+- Soil - PowerSoil DNA Isolation Kit (Qiagen)20
+- Soil - FastDNA Spin kit for soil (MP Bio)21
+- Wastewater samples - Nucleo spin soil DNA kit (Macherey Nagel)22
+- Saliva - OMNIgene ORAL OM-501 (Genotek)23
+- Viral DNA - QIAGEN DNeasy Blood and Tissue Kit (Qiagen)24
+- Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25
+- Microbial DNA - Mo Bio PowerSoil kit (Qiagen)25
+- Phage DNA - QIAamp - DNA stool kit (Qiagen)26
+- Bacterial & Viral DNA - Isolate II Genomic DNA Kit (Bioline)13
+- Fungal DNA - Maxwell® RSC PureFood GMO and Authentication Kit (Promega)27
+- Leaves - PureLink Genomic DNA (ThermoFisher)28
+- Food – Power Food kit (Qiagen)33
+- Mollusc tissues - Qiagen DNeasy Blood and Tissue Kit (Qiagen)34 JV
+- Yogurt - PowerSoil DNA Isolation Kit (MoBio)35 Pamela
+- Saliva - PowerSoil DNA Isolation Kit (MoBio)36, Pamela
+- Plasmid preparations: NucleoSpin Plasmid kit (Macherey-Nagel, Düren, DE)37 Maja
+- Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit38 NT
+- mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit39 NT
+- Bacterial DNA from cultures (automated) - GenFind v3 Kit (Beckman Coulter)40 NT
+- Bacterial DNA from low biomass (eg. FACS sorted) samlpes – mericon DNA Bacteria Kit (Qiagen)41 NT
+
+## RNA extraction
+- Mosquitos - TRIzol LS (Invitrogen) – purified with RNeasy MinElute Cleanup Kit (Qiagen)29
+- Sea Water - RNeasy mini kit (Qiagen)3
+- Antarctic ticks - MagMax mirVana™ Total RNA isolation Kit (ThermoFisher Scientific)30
+- Soil - PowerMax soil DNA isolation kit (Mo Bio)31
+- Cervical samples - Smarter stranded total RNA-seq kit v2—pico input mammalian (Takara Bio)32
+- Viral DNA & RNA - AllPrep DNA/RNA Mini kit (Qiagen)25
+- Viral RNA - QIAmp Viral RNA kit (Qiagen)13
+- Cerebellum, hippocampus and visual cortex - Uneasy Plus Universal Mini Kit (Qiagen)42 JV
+- Bile samples - ZymoBIOMICS DNA/RNA Miniprep Kit43 NT
+- mouse small intestine content - ZymoBIOMICS DNA/RNA Miniprep Kit44 NT
+
+
+##References
+1. Ruocco, N. et al. Microbial diversity in Mediterranean sponges as revealed by metataxonomic analysis. Scientific Reports 2021 11:1 11, 1–12 (2021).
+2. Cebriá-Mendoza, M. et al. Deep viral blood metagenomics reveals extensive anellovirus diversity in healthy humans. Scientific Reports 2021 11:1 11, 1–11 (2021).
+3. Martínez-Pérez, C. et al. Phylogenetically and functionally diverse microorganisms reside under the Ross Ice Shelf. Nature Communications 2022 13:1 13, 1–15 (2022).
+4. Gao, L. et al. Polymicrobial periodontal disease triggers a wide radius of effect and unique virome. npj Biofilms and Microbiomes 2020 6:1 6, 1–13 (2020).
+5. Majumder, R., Sutcliffe, B., Taylor, P. W. & Chapman, T. A. Fruit host-dependent fungal communities in the microbiome of wild Queensland fruit fly larvae. Scientific Reports 2020 10:1 10, 1–12 (2020).
+6. Ellison, S., Knapp, R. & Vredenburg, V. Longitudinal patterns in the skin microbiome of wild, individually marked frogs from the Sierra Nevada, California. ISME Communications 2021 1:1 1, 1–11 (2021).
+7. Kim, H. J. et al. Aged related human skin microbiome and mycobiome in Korean women. Scientific Reports 2022 12:1 12, 1–11 (2022).
+8. Ogai, K. et al. Skin microbiome profile of healthy Cameroonians and Japanese. Scientific Reports 2022 12:1 12, 1–8 (2022).
+9. Chaudhari, D. S. et al. Gut, oral and skin microbiome of Indian patrilineal families reveal perceptible association with age. Scientific Reports 2020 10:1 10, 1–13 (2020).
+10. Scanes, E. et al. Microbiomes of an oyster are shaped by metabolism and environment. Scientific Reports 2021 11:1 11, 1–7 (2021).
+11. Sousa, R. et al. Major ocean currents may shape the microbiome of the topshell Phorcus sauciatus in the NE Atlantic Ocean. Scientific Reports 2021 11:1 11, 1–11 (2021).
+12. Mulec, J. et al. Microbiota entrapped in recently-formed ice: Paradana Ice Cave, Slovenia. Scientific Reports 2021 11:1 11, 1–12 (2021).
+13. Goolam Mahomed, T. et al. Lung microbiome of stable and exacerbated COPD patients in Tshwane, South Africa. Scientific Reports 2021 11:1 11, 1–12 (2021).
+14. Custodio, M. et al. Microbial diversity in intensively farmed lake sediment contaminated by heavy metals and identification of microbial taxa bioindicators of environmental quality. Scientific Reports 2022 12:1 12, 1–12 (2022).
+15. Kursa, O., Tomczyk, G., Sawicka-Durkalec, A., Giza, A. & Słomiany-Szwarc, M. Bacterial communities of the upper respiratory tract of turkeys. Scientific Reports 2021 11:1 11, 1–11 (2021).
+16. Satjarak, A., Golinski, G. K., Trest, M. T. & Graham, L. E. Microbiome and related structural features of Earth’s most archaic plant indicate early plant symbiosis attributes. Scientific Reports 2022 12:1 12, 1–11 (2022).
+17. Park, J. Y. et al. Dysbiotic change in gastric microbiome and its functional implication in gastric carcinogenesis. Scientific Reports 2022 12:1 12, 1–11 (2022).
+18. Eun, Y. G. et al. Oral microbiome associated with lymph node metastasis in oral squamous cell carcinoma. Scientific Reports 2021 11:1 11, 1–10 (2021).
+19. Shetty, S. A. et al. Inter-species Metabolic Interactions in an In-vitro Minimal Human Gut Microbiome of Core Bacteria. npj Biofilms and Microbiomes 2022 8:1 8, 1–13 (2022).
+20. Hannula, S. E. et al. Persistence of plant-mediated microbial soil legacy effects in soil and inside roots. Nature Communications 2021 12:1 12, 1–13 (2021).
+21. Zheng, X. et al. Organochlorine contamination enriches virus-encoded metabolism and pesticide degradation associated auxiliary genes in soil microbiomes. The ISME Journal 2022 16:5 16, 1397–1408 (2022).
+22. Morin, L. et al. Colonization kinetics and implantation follow-up of the sewage microbiome in an urban wastewater treatment plant. Scientific Reports 2020 10:1 10, 1–14 (2020).
+23. Yahara, K. et al. Long-read metagenomics using PromethION uncovers oral bacteriophages and their interaction with host bacteria. Nature Communications 2021 12:1 12, 1–12 (2021).
+24. Lee, C. Z. et al. The gut virome in two indigenous populations from Malaysia. Scientific Reports 2022 12:1 12, 1–10 (2022).
+25. Liang, G. et al. The stepwise assembly of the neonatal virome is modulated by breastfeeding. Nature 2020 581:7809 581, 470–474 (2020).
+26. Chehoud, C. et al. Transfer of viral communities between human individuals during fecal microbiota transplantation. mBio 7, (2016).
+27. Zhang, F. et al. Longitudinal dynamics of gut bacteriome, mycobiome and virome after fecal microbiota transplantation in graft-versus-host disease. Nature Communications 2021 12:1 12, 1–11 (2021).
+28. Humphrey, P. T. & Whiteman, N. K. Insect herbivory reshapes a native leaf microbiome. Nature Ecology & Evolution 2020 4:2 4, 221–229 (2020).
+29. Ali, R. et al. Characterization of the virome associated with Haemagogus mosquitoes in Trinidad, West Indies. Scientific Reports 2021 11:1 11, 1–13 (2021).
+30. Wille, M. et al. Sustained RNA virome diversity in Antarctic penguins and their ticks. The ISME Journal 2020 14:7 14, 1768–1782 (2020).
+31. Xu, L. et al. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nature Communications 2021 12:1 12, 1–17 (2021).
+32. Arroyo Mühr, L. S., Dillner, J., Ure, A. E., Sundström, K. & Hultin, E. Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics. Scientific Reports 2021 11:1 11, 1–12 (2021).
+

docs/_Experimental-Procedure-Standards-SOPs/05-Lipid-and-fatty-acid-extraction-protocol-from-biological-samples.md

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+---
+title: Lipid and fatty acid extraction protocol from biological samples
+category: Experimental-Procedure-Standards-SOPs
+layout: default
+docs_css: markdown
+---
+
+Protocol/MCF/SamplePrep/02: Lipid and fatty acid extraction protocol from biological samples
+
+Aim: Lipid extraction from mammalian cells or microbial samples for LC-MS analysis 
+
+Sample required:
+Cells required: For cultured cells, use the equivalent of 2–3 million cells or 20-30 mg of microbial mass 
+
+Materials:
+MS grade Methanol, Acetonitrile (ACN), Chloroform, Isopropanol (IPA), MilliQ Water, suitable internal standards mix
+Note: Keep diluents in chilled condition (0-4oC)
+
+Procedure for Lipid extraction: 
+MeOH: Chloroform extraction
+(Caution: use only glass vials, syringe.  No plastic items should be in contact with Chloroform)
+1.	Add 200 µL of cold methanol (containing internal standards mix) for 106 cells or 25 mg microbial culture (in 2 mL glass vial)
+2.	Vortex and mix thoroughly for protein precipitation 
+3.	Add 500 µL of chloroform (with glass syringe) and vortex and keep at cold for 10 min 
+4.	Add 200 µL water for phase separation 
+5.	Vortex and keep at cold for 10 min
+6.	Centrifuge at 600 rpm for 5 min (using 15- or 50-mL falcon tubes inserted with glass vials)
+7.	Carefully remove bottom Chloroform layer of 300 µL using syringe and transfer to new amber colour glass vial (with syringe)
+8.	Keep it at speedvac for 20 min at RT or dry under nitrogen gas stream 
+9.	Dried samples can be stored or shipped in dry ice for analysis.
+10.	Reconstitute is dried sample in IPA:MeOH (1:1)
+11.	Blank control: prepare processed blank samples using the same procedure but without biological sample (use water or buffer instead).
+
+
+Note: Method of measurement of cellular/microbial mass should be established with biologist/ microbiologist depending on experimental design. The method can be biomass weight or OD measurements which can be further used for normalization of lipid levels. Similar decision should be made for quenching procedures
+
+Reference:
+Susan S. Bird, Vasant R. Marur, Matthew J. Sniatynski, Heather K. Greenberg, and Bruce S. Kristal., Serum Lipidomics Profiling using LC-MS and High Energy Collisional Dissociation Fragmentation: Focus on Triglyceride Detection and Characterization. Anal Chem. 2011 September 1; 83(17): 6648–6657. doi:10.1021/ac201195d. 
+
+
+
+
+
+Specific instructions for homogenization of frozen tissues (eg; liver) prior to lipid extraction 
+1)	Starting with frozen tissue*, grind the tissue to a powder while frozen using a hand-held ceramic mortar and pestle. The mortar and pestle (any other apparatus eg; tweezers)  should be liquid nitrogen cooled before and should be kept cold throughout the process. A CryoMill can also be used for the homogenization of the tissue. 
+
+2)	Weigh the powder into a tared eppendorf tube. Keep track of the tissue weights as you need to correct for tissue weight (normalize) when resuspending the samples prior to LC-MS analysis
+
+3)	Extract lipids using the method above Protocol/MCF/SamplePrep/02 
+
+4)	Re-extraction: After the initial extraction, perform a second extraction step of the tissue with 2:1 Chloroform: Methanol (~ 700μL) and combine the bottom layer with the layer from step 3. 
+
+5)	Dry the bottom layer under a nitrogen stream.
+
+*It is difficult to process tissue samples at weights below 10 mg, so aim for at least 10 mg of tissue to start with 
+
+

docs/_Experimental-Procedure-Standards-SOPs/06-Metabolite-extraction-from-adherent-mammalian-cells.md

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+---
+title: Metabolite extraction from adherent mammalian cells
+category: Experimental-Procedure-Standards-SOPs
+layout: default
+docs_css: markdown
+---
+
+Protocol/MCF/SamplePrep/01: Metabolite extraction from adherent mammalian cells 
+
+Aim: Aqueous metabolite extraction from mammalian cells or microbial samples for LC-MS analysis 
+
+Sample required:
+Cells required: Cells For cultured cells, use the equivalent of 2–3 million cells. For other sample types a minimum mass of 20 mg is required.
+
+Materials:
+MS grade Methanol (with suitable IS mix 100 ng), MilliQ Water, with suitable internal standards mix 100 ng
+
+Note: Keep diluents in chilled condition (0-4oC)  
+Sample preparation and metabolite extraction:
+
+1.	Take 250μl spent growth medium and place it in Eppendorf tubes which already contain 750μl very cold (-80oC) HPLC-grade methanol. (Keep it in case you wish to analyze extracellular metabolites). [optional]
+2.	Aspirate the medium completely.
+3.	Pour 10ml (adjust volume as per the size of dish/ plate) of 10 mM Ammonium acetate (all over the petri dish, wash cells carefully and gently and then discard the washing solution.
+4.	Put the plates on dry ice and add 4 ml of 80% (vol/vol) methanol (or Methanol:acetonitrile:water; 4:4:2) (cooled to - 80°C or on dry ice or liquid nitrogen). (adjust volume as per the size of dish/ plate)
+5.	Incubate the plate at - 80 °C for 20 min. Remove cell plate and keep it on dry ice.
+6.	Scrape the plates on dry ice with cell scraper.
+7.	Transfer the cell lysate/methanol mixture to a 15 ml conical tube (or 1.5 ml / 5 ml eppendorf depending on volumes) on dry ice. If you notice residual cells on the plate, introduce additional washing steps to increase the yield and reduce inter-sample variability
+8.	Add appropriate internal standards
+9.	Vortex for 5 min at maximum speed and make sure that pellet disintegrates and mixed thoroughly with extraction solvent.
+10.	Sample lysis and homogenization (discuss details and alternatives with MCF member). Simplest procedure: place the samples in an ultrasonication bath and sonicate the sample tube for 5 min (Note: Put some ice in sonicator water bath to avoid heating of sample during sonication; rotate/change position of samples during sonication as the energy is not homogeneously distributed in most ultrasonication baths) and vortex briefly after sonication.
+11.	Centrifuge the tube at 14,000g for 10 min at 4–8 °C to pellet the cell debris.
+12.	Transfer the metabolite-containing supernatant to a new 15-ml conical tube (or 1.5 ml eppendorf) on dry ice.
+13.	Optional re-extraction step: Add 500 μl 80% (vol/vol) methanol (- 80°C) to the pellet and resuspend in a 1.5 ml tube and vortex for 1 min.
+○	Resuspending the pellet may be difficult and may require a combination ofvortexing and pipetting up and down (or short period (5 sec) of ultrasonication)
+14.	Spin the tubes at 14,000g for 10 min at 4–8 °C.
+15.	Transfer the supernatant to a tube on dry ice (from Step 13).Divide and transfer 4.5 ml of total extraction buffer into three 1.5-ml microcentrifuge tubes (1.5 ml in each tube). [This step is optional, extracts can be dried directly]
+
+16.	SpeedVac/lyophilize or dry under nitrogen gas to a pellet using no heat.
+17.	Submit dried sample in 1.5 ml eppendorf tube and can be stored at in dried ice.
+18.	Blank control: prepare processed blank sample using same procedure but without biological sample (use water or buffer instead). 
+
+Reference:
+1.	Yuan M, Breitkopf SB, Yang X, Asara JM. A positive/negative ion-switching, targeted mass spectrometry-based metabolomics platform for bodily fluids, cells, and fresh and fixed tissue. Nat Protoc. 2012 Apr 12;7(5):872-81. doi: 10.1038/nprot.2012.024.
+

docs/_Experimental-Procedure-Standards-SOPs/07-Metabolite-extraction-from-plant-tissue.md

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+---
+title: Metabolite extraction from plant tissue
+category: Experimental-Procedure-Standards-SOPs
+layout: default
+docs_css: markdown
+---
+
+
+Protocol/MCF/SamplePrep/03: Metabolite extraction from plant tissues  
+
+Sample required:Plant material required: 20-50 mg finely homogenized tissue 
+
+Materials and preparations:
+MS grade Methanol (with suitable IS mix 100 ng), MilliQ Water, with suitable internal standards mix 100 ng, HLB (30 mg) SPE columns, SPE assembly, 5% Methanol, 80% methanol 
+Extraction buffer (50 mM sodium phosphate buffer, pH 7.0, containing 0.1%diethyldithiocarbamate)Loading bufferUse 1 ml of the extraction buffer to test the amount of 1M HCl needed for itsacidification to pH 2.7. Prepare the loading buffer by adding twice the amount of1 M HCl per milliliter of extraction buffer. (Addition of 0.5 ml sample extract to 0.5 ml loading buffer must give a pH 2.7)
+
+Note: Keep diluents in chilled condition (0-4oC)  
+
+Sample preparation and metabolite extraction:
+
+1.	Sample Extraction (For Indole acetate metabolites; IAA):  20 to 50 mg of tissues was mixed with 1 ml cold extraction buffer and homogenized using a Mixer Mill MM301 bead mill (Retsch GmbH (http://www.retsch.com)) at a frequency of 25 Hz for 5 min after adding 2 mm ceria-stabilized zirconium oxide beads.
+2.	Add 1 μg of 13C indole acetate (or other suitable internal standards) and vortex well.
+3.	Incubated this plant extracts at 4°C with continuous shaking (20 min) and centrifuge (15 min, 23 000 g at 4°C)
+4.	Transfer the supernatant to a new vial and adjust pH to 2.7 with 1 M HCl
+5.	SPE procedure:
+a.	Prepare SPE vacuum assembly with HLB (30mg) column cartridges.  
+b.	Condition SPE column with 1 mL of methanol and 1mL of water
+c.	Equilibrate the column with 250 μl of 5 mM HCl. (Do not let column dry)
+d.	Load equilibrate column with 0.5 ml loading buffer 
+e.	Load 0.5 ml Sample onto the SPE column, and mix intensely with the loading buffer. Pass the mixture slowly through the HLB sorbent immediately.
+f.	Wash the column with 2 ml of 5% methanol.
+g.	Put clean glass tubes into the manifold rack, and then elute the sample from the column with 2 ml of 80% methanol.
+h.	Collect sample eluent and evaporate the samples to dryness in a SpeedVac concentrator or under nitrogen stream at room temperature.
+6.	Store samples at -80°C till further analysis or ship in dry ice.
+
+7.	Sample are reconstituted in mobile phase (or 50% methanol) before analysis 
+
+
+
+Reference:
+1.	Nov´ak, O., Pˇenˇc´ık, A., Blahouˇsek, O., and Ljung, K. 2016.Quantitative auxin metabolite profiling using stable isotope dilutionUHPLC-MS/MS. Curr. Protoc. Plant Biol. 1:419-430. doi: 10.1002/cppb.20028