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| Name | Authors | DOI | Group |
Summary |
Associated Publications |
RRIDs used | ||||||
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MTN100 with 5x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.ded3a5 | VERVE Net, Sullivan Lab | This mixture is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 5x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.ded3a5 | 2021-04-15 09:14:33 | |||
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Isolation of cyanophages by liquid enrichment assay Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dp65rd | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Another convenient way to screen larger sample volumes is to perform liquid enrichment cultures (Suttle 1993). By this approach, larger volumes of water samples can be screened for cyanophages, thus enabling detection of “rare” viruses. Similar to the use of enrichment cultures for bacteriophages, the disadvantages include the fact that lysis of the host cells are not always obvious, especially if the initial titer is low or if the host culture is not clonal or unialgal. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Isolation of cyanophages by liquid enrichment assay. protocols.io https://dx.doi.org/10.17504/protocols.io.dp65rd | 2021-04-15 09:14:33 | ||
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Obtaining pure cyanophage stocks (liquid assay) Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dqm5u5 | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Obtaining pure cyanophage stocks (liquid assay). protocols.io https://dx.doi.org/10.17504/protocols.io.dqm5u5 | 2021-04-15 09:14:29 | |||
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BG-11 Medium for Freshwater Cyanobacteria Resource Report Resource Website |
Li Deng | DOI:10.17504/protocols.io.ddd225 | VERVE Net, Sullivan Lab | This medium is used successfully for most cyanobacteria. Vitamin B12 may be added for those species that require it. Use f/2 vitamin solution. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Li Deng 2016. BG-11 Medium for Freshwater Cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.ddd225 | 2021-04-15 09:14:30 | |||
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Cyanophage plaque purification Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c3yypv | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. Cyanophage plaque purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3yypv | 2021-04-15 09:14:38 | ||||
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Extracting DNA from viruses embedded in agarose Resource Report Resource Website |
Grieg F. Steward and Alexander I. Culley | DOI:10.17504/protocols.io.dsd6a5 | VERVE Net, Culley Lab_ULaval | If one wishes to have a stock of high molecular weight viral DNA that can be stored for long periods of time with minimal shearing or degradation, the viruses can be embedded in agarose before extraction. Extraction of embedded cells is the standard procedure for sizing the genomes of bacteria and yeast by PFGE (Sambrook and Russell 2001), and a similar protocol can be used for embedded viruses (Rohozinski et al. 1989; Lanka et al. 1993; Wommack et al. 1999; Sandaa et al. 2010, this volume).This is a protocol from: Steward, G. F. and A. I. Culley. 2010. Chapter 16: Extraction and purification of nucleic acids from viruses. Manual of Aquatic Viral Ecology. Waco, TX:American Society of Limnology and Oceanography. doi:10.4319/mave.2010.978-0-9845591-0-7Please see the published manuscript for additional information. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_154.pdf | 1 | 2015 | Grieg F. Steward and Alexander I. Culley 2015. Extracting DNA from viruses embedded in agarose. protocols.io https://dx.doi.org/10.17504/protocols.io.dsd6a5 | 2021-04-15 09:14:29 | ||
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Lysin purification protocol Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.et3beqn | VERVE Net | University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Lysin purification protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.et3beqn | 2021-04-15 09:14:37 | ||||
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MTN100 with 3x NaCl Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.dee3bd | VERVE Net, Sullivan Lab | This mixture is is used with Cesium Chloride Dialysis for Viruses | University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. MTN100 with 3x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.dee3bd | 2021-04-15 09:14:28 | |||
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Script P8: Phage Replication Cycle Resource Report Resource Website |
HANNIGAN GD, GRICE EA, ET AL. | DOI:10.17504/protocols.io.egwbbxe | VERVE Net, Club Grice | This protocol provides a method for predicting the proportions of phage replication cycles within the skin virome. We will be looking at three markers for temperate phages: 1) presence of integrase genes, 2) presence of ACLAME database prophage elements, and 3) similarity to bacterial genomes. Based on the methods found in the following publication: Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." mBio 6.5 (2015): e01578-15. | Kindler L, Stoliartchouk A, Teytelman L, Hurwitz BL, Method-centered digital communities on protocols.io for fast-paced scientific innovation. F1000Research doi: 10.12688/f1000research.9453.2 | DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA, DEPARTMENT OF DERMATOLOGY UNIVERSITY OF PENNSYLVANIA | http://mbio.asm.org/content/6/5/e01578-15.full | 1 | 2016 | HANNIGAN GD, GRICE EA, ET AL. 2016. Script P8: Phage Replication Cycle. protocols.io https://dx.doi.org/10.17504/protocols.io.egwbbxe | 2021-04-15 09:14:30 | |
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Preparation of NC64A “Ghosts” Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.eudbes6 | VERVE Net | The University of Nebraska-Lincoln | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Preparation of NC64A “Ghosts”. protocols.io https://dx.doi.org/10.17504/protocols.io.eudbes6 | 2021-04-15 09:14:42 | ||||
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Phenol extraction of proteins Resource Report Resource Website |
David Dunigan and Irina Agarkova | DOI:10.17504/protocols.io.esgbebw | VERVE Net | University of Nebraska-Lincoln | http://lclane.net/text/phenol.html | 1 | 2016 | David Dunigan and Irina Agarkova 2016. Phenol extraction of proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.esgbebw | 2021-04-15 09:14:42 | |||
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Isolation and life cycle characterization of lytic viruses infecting heterotrophic bacteria and cyanobacteria Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dxq7mv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | This collection presents some of the most widely used methodological approaches for isolation and purification of bacteriophages and cyanophages, the first step in detailed studies of virus–host interactions and viral genetic composition, and discusses the applications and limitations of different isolation procedures. Most work on phage isolation has been carried out with aerobic heterotrophic bacteria and cyanobacteria, culturable both on agar plates and in enriched liquid cultures. The procedures presented here are limited to lytic viruses infecting such hosts. In addition to the isolation procedures, methods for life cycle characterization (one-step growth experiments) of bacteriophages and cyanophages are described. | , , | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Isolation and life cycle characterization of lytic viruses infecting heterotrophic bacteria and cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.dxq7mv | 2021-04-15 09:14:33 | |||
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Isolation of DNA from phage lysate Resource Report Resource Website |
Natalie Solonenko | DOI:10.17504/protocols.io.c36yrd | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Natalie Solonenko 2016. Isolation of DNA from phage lysate. protocols.io https://dx.doi.org/10.17504/protocols.io.c36yrd | 2021-04-15 09:14:46 | ||||
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Obtaining pure phage stock Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dpu5nv | VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology | Clearing zones on lawns of host bacteria potentially contain all lytic phages against the given host that were present in the original water sample. Little is still known about the occurrence and diversity of phages infecting specific hosts, but generally isolation procedures as those described above may reveal multiple phages against specific target bacteria (e.g., Comeau et al. 2006; Holmfeldt et al. 2007; Stenholm et al. 2008). It is therefore necessary to further isolate the phages to obtain specific stocks of single phages. | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_118.pdf | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Obtaining pure phage stock. protocols.io https://dx.doi.org/10.17504/protocols.io.dpu5nv | 2021-04-15 09:14:51 | ||
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Liquid Amplification Resource Report Resource Website |
Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen | DOI:10.17504/protocols.io.dq65zd | VERVE Net | For use in "Obtaining pure cyanophage stock: plaque purification" | Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology, Manual of Aquatic Viral Ecology | 1 | 2016 | Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Liquid Amplification. protocols.io https://dx.doi.org/10.17504/protocols.io.dq65zd | 2021-04-15 09:14:36 | |||
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Non-Centrifuged Plaque Assay Sample Steps Resource Report Resource Website |
Matthew Sullivan | DOI:10.17504/protocols.io.der3d5 | VERVE Net, Sullivan Lab | For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol. | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2016 | Matthew Sullivan 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.der3d5 | 2021-04-15 09:14:47 | |||
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Virus nucleic acids extractions from 0.02 µm anotop filters Resource Report Resource Website |
Jozef Nissimov | DOI:10.17504/protocols.io.d9m945 | VERVE Net, Bidle Lab | This protocol has been modified from the original method developed and reported by Steward and Culley (2010) and Mueller et al. (2014). As a starting point we assume that viruses have been collected from the environment on 0.02 µm syringe filters (Anotop, Whatman). | DMCS, Rutgers University | 1 | 2015 | Jozef Nissimov 2015. Virus nucleic acids extractions from 0.02 µm anotop filters. protocols.io https://dx.doi.org/10.17504/protocols.io.d9m945 | 2021-04-15 09:14:36 | |||
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Separation of free virus particles from sediments in aquatic systems Resource Report Resource Website |
Roberto Danovaro and Mathias Middelboe | DOI:10.17504/protocols.io.dpg5jv | VERVE Net, Middelboe Lab | This protocol is for the separation of free virus particles from sediments. It is from:Danovaro, R., and M. Middelboe. 2010. Separation of free virus particles from sediments in aquatic systems, p. 74–81. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.Please see the full chapter for additional details. | Manual of Aquatic Viral Ecology | http://www.aslo.org/books/mave/MAVE_074.pdf | 1 | 2016 | Roberto Danovaro and Mathias Middelboe 2016. Separation of free virus particles from sediments in aquatic systems. protocols.io https://dx.doi.org/10.17504/protocols.io.dpg5jv | 2021-04-15 09:14:53 | ||
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0.5M EDTA Resource Report Resource Website |
Matthew Sullivan Lab | DOI:10.17504/protocols.io.c58y9v | VERVE Net, Sullivan Lab | Matthew Sullivan Lab, University of Arizona, Ohio State University | 1 | 2015 | Matthew Sullivan Lab 2015. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c58y9v | 2021-04-15 09:14:53 | ||||
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Chlorella Virus Plaque Assay Resource Report Resource Website |
Steven Wilhelm | DOI:10.17504/protocols.io.ge2btge | VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs) | Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/ | The University of Tennessee, Knoxville | http://ncv.unl.edu/vanettenlab/Plaque%20assay.pdf | 1 | 2016 | Steven Wilhelm 2016. Chlorella Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.ge2btge | 2021-04-15 09:14:39 |
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