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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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Concentrating Viruses by Tangential Flow Filtration Resource Report Resource Website |
Dr. Steven Wilhelm, Samantha Coy | 10.17504/protocols.io.hgrb3v6 | VERVE Net, The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Samantha R Coy's Protocols | 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. | , | 2 | 2017 | Dr. Steven Wilhelm, Samantha Coy 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io dx.doi.org/10.17504/protocols.io.hgrb3v6 | 2021-03-29 03:07:53 | |||
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RNA extraction from Sterivex using phenol:chloroform - cutting off the filter from the Sterivex unit for low biomass samples Resource Report Resource Website |
Naomi Gilbert, Helena Pound, Steven Wilhelm | 10.17504/protocols.io.bh75j9q6 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 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. | The University of Tennessee, Knoxville, University of Tennessee, Knoxville, The University of Tennessee, Knoxville | 1 | 2020 | 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 | 2021-03-29 03:08:02 | |||
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BG-11 Trace metal mix A5 Resource Report Resource Website |
Dr. Steven Wilhelm | 10.17504/protocols.io.h92b98e | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | 2 | 2017 | Dr. Steven Wilhelm 2017. BG-11 Trace metal mix A5. protocols.io dx.doi.org/10.17504/protocols.io.h92b98e | 2021-03-29 03:08:16 | ||||
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Biohazard Garbage Protocol: Autoclave Biohazard Waste Resource Report Resource Website |
Steven Wilhelm, Gary Lecleir | 10.17504/protocols.io.6cyhaxw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | The University of Tennessee, Knoxville, The University of Tennessee, Knoxville | 1 | 2019 | Steven Wilhelm, Gary Lecleir 2019. Biohazard Garbage Protocol: Autoclave Biohazard Waste. protocols.io dx.doi.org/10.17504/protocols.io.6cyhaxw | 2021-03-29 03:08:21 | ||||
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Quantifying Biogenic Silica (bSi) Deposition Rates Adapted Method & Fluorescence Reading (PDMPO) via Fluorometer Resource Report Resource Website |
Brittany Zepernick, Matthew Saxton, Steven Wilhelm | 10.17504/protocols.io.735hqq6 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health | 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. | University of Tennessee, Knoxville, Miami University of Ohio, The University of Tennessee, Knoxville | http://wilhelmlab.utk.edu/ | 1 | 2019 | 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 | 2021-03-29 03:07:41 | ||
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Bacteriophage Cryopreservation Resource Report Resource Website |
Dr. Steven Wilhelm | 10.17504/protocols.io.iiyccfw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | 1 | 2017 | Dr. Steven Wilhelm 2017. Bacteriophage Cryopreservation. protocols.io dx.doi.org/10.17504/protocols.io.iiyccfw | 2021-03-29 03:11:29 | ||||
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Cleaning up a biohazardous spill inside a centrifuge Resource Report Resource Website |
Steven Wilhelm, Gary Lecleir, Ashley Humphrey | 10.17504/protocols.io.wgkfbuw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | BIOLOGICAL SPILL RESPONSE method to be used in the event of a biosafety incident. | The University of Tennessee, Knoxville, The University of Tennessee, Knoxville, University of Tennessee, Knoxville | 1 | 2019 | 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 | 2021-03-29 03:13:27 | |||
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Reading Sample Fluorescence (PDMPO) via Fluorometer Resource Report Resource Website |
Brittany Zepernick, Matthew Saxton, Steven Wilhelm | 10.17504/protocols.io.72whqfe | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health | University of Tennessee, Knoxville, Miami University of Ohio, The University of Tennessee, Knoxville | http://wilhelmlab.utk.edu/ | 1 | 2019 | Brittany Zepernick, Matthew Saxton, Steven Wilhelm 2019. Reading Sample Fluorescence (PDMPO) via Fluorometer. protocols.io dx.doi.org/10.17504/protocols.io.72whqfe | 2021-03-29 03:13:31 | |||
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Plaque Assay for the Aureococcus anophagefferens Virus (AaV) Resource Report Resource Website |
Eric Gann | 10.17504/protocols.io.g2nbyde | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 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. | http://rdcu.be/oJCt | 1 | 2017 | Eric Gann 2017. Plaque Assay for the Aureococcus anophagefferens Virus (AaV). protocols.io dx.doi.org/10.17504/protocols.io.g2nbyde | 2021-03-29 03:13:41 | |||
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Concentrating Viruses by Tangential Flow Filtration Resource Report Resource Website |
Steven Wilhelm | 10.17504/protocols.io.grrbv56 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 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. | The University of Tennessee, Knoxville | 1 | 2017 | Steven Wilhelm 2017. Concentrating Viruses by Tangential Flow Filtration. protocols.io dx.doi.org/10.17504/protocols.io.grrbv56 | 2021-03-29 03:13:45 | |||
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Cleaning up a biohazardous spill outside of a biosafety cabinet Resource Report Resource Website |
Steven Wilhelm, Gary Lecleir, Ashley Humphrey | 10.17504/protocols.io.wgjfbun | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | BIOLOGICAL SPILL RESPONSE method to be used in the event of a biosafety incident. | The University of Tennessee, Knoxville, The University of Tennessee, Knoxville, University of Tennessee, Knoxville | 1 | 2019 | 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 | 2021-03-29 03:12:40 | |||
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Phenol/chloroform extraction of DNA from cyanobacteria Resource Report Resource Website |
Robbie Martin, Steven W. Wilhelm | 10.17504/protocols.io.mszc6f6 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 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. | University of Tennessee, Knoxville, University of Tennessee, Knoxville | 1 | 2018 | Robbie Martin, Steven W. Wilhelm 2018. Phenol/chloroform extraction of DNA from cyanobacteria. protocols.io dx.doi.org/10.17504/protocols.io.mszc6f6 | 2021-03-29 03:12:51 | |||
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Guava Flow Cytometry Resource Report Resource Website |
Dr. Steven Wilhelm, Alyssa Alsante | 10.17504/protocols.io.ikyccxw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | , | 1 | 2017 | Dr. Steven Wilhelm, Alyssa Alsante 2017. Guava Flow Cytometry. protocols.io dx.doi.org/10.17504/protocols.io.ikyccxw | 2021-03-29 03:14:54 | |||
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Fe-EDTA Stock solution for ESAW Media for Marine Phytoplankton Resource Report Resource Website |
Ashley Humphrey | 10.17504/protocols.io.getbten | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Fe-EDTA Stock Solution for ESAW Media for Marine Phytoplankton | University of Tennessee, Knoxville | 1 | 2016 | Ashley Humphrey 2016. Fe-EDTA Stock solution for ESAW Media for Marine Phytoplankton. protocols.io dx.doi.org/10.17504/protocols.io.getbten | 2021-03-29 03:14:57 | |||
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Phenol Chloroform DNA extraction from polycarbonate filters Resource Report Resource Website |
Ashley Humphrey | 10.17504/protocols.io.ibbcain | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), CyanoHABs | University of Tennessee, Knoxville | 1 | 2017 | Ashley Humphrey 2017. Phenol Chloroform DNA extraction from polycarbonate filters. protocols.io dx.doi.org/10.17504/protocols.io.ibbcain | 2021-03-29 03:12:58 | ||||
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Transformation of Aureococcus anophagefferens by Electroporation Resource Report Resource Website |
Eric Gann | 10.17504/protocols.io.g2vbye6 | Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 1 | 2017 | Eric Gann 2017. Transformation of Aureococcus anophagefferens by Electroporation. protocols.io dx.doi.org/10.17504/protocols.io.g2vbye6 | 2021-03-29 03:13:02 | |||||
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Running the Thermo Scientific Arktik Thermal Cycler Resource Report Resource Website |
Dr. Steven Wilhelm, Alyssa Alsante | 10.17504/protocols.io.in5cdg6 | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | , | 1 | 2017 | Dr. Steven Wilhelm, Alyssa Alsante 2017. Running the Thermo Scientific Arktik Thermal Cycler. protocols.io dx.doi.org/10.17504/protocols.io.in5cdg6 | 2021-03-29 03:15:27 | |||
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Plaque Assay For Screening Viral Concentrates for Bacteriophage Resource Report Resource Website |
Dr. Steven Wilhelm | 10.17504/protocols.io.igxcbxn | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Please contact Dr. Steven Wilhelm ([email protected]) for additional information regarding this protocol. | 1 | 2017 | Dr. Steven Wilhelm 2017. Plaque Assay For Screening Viral Concentrates for Bacteriophage. protocols.io dx.doi.org/10.17504/protocols.io.igxcbxn | 2021-03-29 03:12:27 | ||||
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Metatranscriptomic screening for genes of interest Resource Report Resource Website |
Helena Pound, Steven Wilhelm | 10.17504/protocols.io.7vyhn7w | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs), Great Lakes Center for Fresh Waters and Human Health | Find genes of interest in assembled metatranscriptomic library using blast. | University of Tennessee, Knoxville, The University of Tennessee, Knoxville | http://wilhelmlab.utk.edu/ | 1 | 2019 | Helena Pound, Steven Wilhelm 2019. Metatranscriptomic screening for genes of interest. protocols.io dx.doi.org/10.17504/protocols.io.7vyhn7w | 2021-03-29 03:12:29 | ||
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Epifluorescent Microscopy of Virus Particles Using SYBR Green Resource Report Resource Website |
Dr. Steven Wilhelm, Samantha Coy | 10.17504/protocols.io.hg4b3yw | The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | 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. | , | 2 | 2017 | Dr. Steven Wilhelm, Samantha Coy 2017. Epifluorescent Microscopy of Virus Particles Using SYBR Green. protocols.io dx.doi.org/10.17504/protocols.io.hg4b3yw | 2021-03-29 03:12:35 |
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