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Authors: Dr. Steven Wilhelm, Samantha Coy
Group: VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols
Summary: Ultracentrifugation in the WX Ultra Series can support only 30 mL samples at a time, and therefore do not significantly concentrate viruses. Tangential flow filtration enables viral concentration of large volumes that can then be purified using sucrose density gradients. Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io dx.doi.org/10.17504/protocols.io.hgrb3v6 Copy
Authors: Naomi Gilbert, Helena Pound, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: This extraction protocol uses a modified filter extraction method and bead-beating technique. This verison uses a technique to attempt to increase the biomass recovered from low-biomass samples by cutting out the filter from the sterivex unit with a sterile razor blade or scalpel. The filter is then placed directly into the bead bashing lysis tube and is homogenized with the starting solution. The protocol has been tested and used on oligotrophic seawater samples that contain a low amount of biomass.
Proper citation: Naomi Gilbert, Helena Pound, Steven Wilhelm 2020. RNA extraction from Sterivex using phenol:chloroform - cutting off the filter from the Sterivex unit for low biomass samples. protocols.io dx.doi.org/10.17504/protocols.io.bh75j9q6 Copy
Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm 2017. BG-11 Trace metal mix A5. protocols.io dx.doi.org/10.17504/protocols.io.h92b98e Copy
Authors: Steven Wilhelm, Gary Lecleir
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Proper citation: Steven Wilhelm, Gary Lecleir 2019. Biohazard Garbage Protocol: Autoclave Biohazard Waste. protocols.io dx.doi.org/10.17504/protocols.io.6cyhaxw Copy
Authors: Brittany Zepernick, Matthew Saxton, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health
Summary: This method can be used to assess and quantify the rate of silica deposition (bSi) over time in diatoms to determine their rate of frustule synthesis. This protocol has been adapted for the processing of both cultures as well as environmental samples when inoculated with PDMPO [2‐(4‐pyridyl)‐5‐((4‐(2dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole], which is a fluorescent dye that is co-deposited with silica during frustule biosynthesis in a 3230:1 Si:PDMPO (mol:mol) ratio.
Proper citation: Brittany Zepernick, Matthew Saxton, Steven Wilhelm 2019. Quantifying Biogenic Silica (bSi) Deposition Rates Adapted Method & Fluorescence Reading (PDMPO) via Fluorometer. protocols.io dx.doi.org/10.17504/protocols.io.735hqq6 Copy
Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm 2017. Bacteriophage Cryopreservation. protocols.io dx.doi.org/10.17504/protocols.io.iiyccfw Copy
Authors: Steven Wilhelm, Gary Lecleir, Ashley Humphrey
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: BIOLOGICAL SPILL RESPONSE method to be used in the event of a biosafety incident.
Proper citation: Steven Wilhelm, Gary Lecleir, Ashley Humphrey 2019. Cleaning up a biohazardous spill inside a centrifuge. protocols.io dx.doi.org/10.17504/protocols.io.wgkfbuw Copy
Authors: Brittany Zepernick, Matthew Saxton, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health
Proper citation: Brittany Zepernick, Matthew Saxton, Steven Wilhelm 2019. Reading Sample Fluorescence (PDMPO) via Fluorometer. protocols.io dx.doi.org/10.17504/protocols.io.72whqfe Copy
Authors: Eric Gann
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: We have developed a plaque assay for AaV with a modified protocol from Schroeder et. al 2002. Protocol modified from:Schroeder, D.C., et al., Coccolithovirus (Phycodnaviridae): Characterisation of a new large dsDNAalgal virus that infects Emiliania huxleyi. Archives of Virology, 2002.147(9): p. 1685-1698.
Proper citation: Eric Gann 2017. Plaque Assay for the Aureococcus anophagefferens Virus (AaV). protocols.io dx.doi.org/10.17504/protocols.io.g2nbyde Copy
Authors: Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Ultracentrifugation in the WX Ultra Series can support only 30 mL samples at a time, and therefore do not significantly concentrate viruses. Tangential flow filtration enables viral concentration of large volumes that can then be purified using sucrose density gradients.
Proper citation: Steven Wilhelm 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io dx.doi.org/10.17504/protocols.io.grrbv56 Copy
Authors: Steven Wilhelm, Gary Lecleir, Ashley Humphrey
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: BIOLOGICAL SPILL RESPONSE method to be used in the event of a biosafety incident.
Proper citation: Steven Wilhelm, Gary Lecleir, Ashley Humphrey 2019. Cleaning up a biohazardous spill outside of a biosafety cabinet. protocols.io dx.doi.org/10.17504/protocols.io.wgjfbun Copy
Authors: Robbie Martin, Steven W. Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Phenol/chloroform-based DNA extraction from cells pre-treated with RNase A, lysozyme, proteinase K, and SDS. The protocol was optimized for extracting DNA from Microcystis aeruginosa, but works well for other cyanobacteria.
Proper citation: Robbie Martin, Steven W. Wilhelm 2018. Phenol/chloroform extraction of DNA from cyanobacteria. protocols.io dx.doi.org/10.17504/protocols.io.mszc6f6 Copy
Authors: Dr. Steven Wilhelm, Alyssa Alsante
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Alyssa Alsante 2017. Guava Flow Cytometry. protocols.io dx.doi.org/10.17504/protocols.io.ikyccxw Copy
Authors: Ashley Humphrey
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Fe-EDTA Stock Solution for ESAW Media for Marine Phytoplankton
Proper citation: Ashley Humphrey 2016. Fe-EDTA Stock solution for ESAW Media for Marine Phytoplankton. protocols.io dx.doi.org/10.17504/protocols.io.getbten Copy
Authors: Ashley Humphrey
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs
Proper citation: Ashley Humphrey 2017. Phenol Chloroform DNA extraction from polycarbonate filters. protocols.io dx.doi.org/10.17504/protocols.io.ibbcain Copy
Authors: Eric Gann
Group: Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Proper citation: Eric Gann 2017. Transformation of Aureococcus anophagefferens by Electroporation. protocols.io dx.doi.org/10.17504/protocols.io.g2vbye6 Copy
Authors: Dr. Steven Wilhelm, Alyssa Alsante
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Alyssa Alsante 2017. Running the Thermo Scientific Arktik Thermal Cycler. protocols.io dx.doi.org/10.17504/protocols.io.in5cdg6 Copy
Authors: Dr. Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm 2017. Plaque Assay For Screening Viral Concentrates for Bacteriophage. protocols.io dx.doi.org/10.17504/protocols.io.igxcbxn Copy
Authors: Helena Pound, Steven Wilhelm
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health
Summary: Find genes of interest in assembled metatranscriptomic library using blast.
Proper citation: Helena Pound, Steven Wilhelm 2019. Metatranscriptomic screening for genes of interest. protocols.io dx.doi.org/10.17504/protocols.io.7vyhn7w Copy
Authors: Dr. Steven Wilhelm, Samantha Coy
Group: The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Adapted from: Ortmann and Suttle (2009) Determination of Virus Abundance by Epifluorescence microscopy. Ch. 10 Methods of Molecular Biology. Contact Dr. Steven Wilhelm ([email protected]) or Samantha Coy ([email protected]) for additional information regarding this protocol.
Proper citation: Dr. Steven Wilhelm, Samantha Coy 2017. Epifluorescent Microscopy of Virus Particles Using SYBR Green. protocols.io dx.doi.org/10.17504/protocols.io.hg4b3yw Copy
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