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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used with Cesium Chloride Dialysis for Viruses

Proper citation: Matthew Sullivan 2016. MTN100 with 5x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.ded3a5 Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: 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.

Proper citation: 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 Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology

Proper citation: 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 Copy   

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Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: This medium is used successfully for most cyanobacteria. Vitamin B12 may be added for those species that require it. Use f/2 vitamin solution.

Proper citation: Li Deng 2016. BG-11 Medium for Freshwater Cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.ddd225 Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan Lab 2015. Cyanophage plaque purification. protocols.io https://dx.doi.org/10.17504/protocols.io.c3yypv Copy   

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Authors: Grieg F. Steward and Alexander I. Culley
Group: VERVE Net, Culley Lab_ULaval
Summary: 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.

Proper citation: 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 Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Lysin purification protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.et3beqn Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: This mixture is is used with Cesium Chloride Dialysis for Viruses

Proper citation: Matthew Sullivan 2016. MTN100 with 3x NaCl. protocols.io https://dx.doi.org/10.17504/protocols.io.dee3bd Copy   

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Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: 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.

Proper citation: HANNIGAN GD, GRICE EA, ET AL. 2016. Script P8: Phage Replication Cycle. protocols.io https://dx.doi.org/10.17504/protocols.io.egwbbxe Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Preparation of NC64A “Ghosts”. protocols.io https://dx.doi.org/10.17504/protocols.io.eudbes6 Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Phenol extraction of proteins. protocols.io https://dx.doi.org/10.17504/protocols.io.esgbebw Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: 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.

Proper citation: 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 Copy   

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Authors: Natalie Solonenko
Group: VERVE Net, Sullivan Lab

Proper citation: Natalie Solonenko 2016. Isolation of DNA from phage lysate. protocols.io https://dx.doi.org/10.17504/protocols.io.c36yrd Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: 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.

Proper citation: 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 Copy   

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Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net
Summary: For use in "Obtaining pure cyanophage stock: plaque purification"

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Liquid Amplification. protocols.io https://dx.doi.org/10.17504/protocols.io.dq65zd Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.

Proper citation: Matthew Sullivan 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.der3d5 Copy   

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Authors: Jozef Nissimov
Group: VERVE Net, Bidle Lab
Summary: 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).

Proper citation: Jozef Nissimov 2015. Virus nucleic acids extractions from 0.02 µm anotop filters. protocols.io https://dx.doi.org/10.17504/protocols.io.d9m945 Copy   

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Authors: Roberto Danovaro and Mathias Middelboe
Group: VERVE Net, Middelboe Lab
Summary: 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.

Proper citation: 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 Copy   

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Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan Lab 2015. 0.5M EDTA. protocols.io https://dx.doi.org/10.17504/protocols.io.c58y9v Copy   

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Authors: Steven Wilhelm
Group: VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G), The Aquatic Microbial Ecology Research Group - AMERG (The Buchan, Zinser and Wilhelm labs)
Summary: Adapted from: Van Etten, J. (n.d.). Titering of Chlorella Viruses. Retrieved from http://ncv.unl.edu/vanettenlab/

Proper citation: Steven Wilhelm 2016. Chlorella Virus Plaque Assay. protocols.io https://dx.doi.org/10.17504/protocols.io.ge2btge Copy   

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