Protocols   Select Another Resource Report Type

Authors: Matthias Fischer
Group: VERVE Net, Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: The concentration and purification of giant DNA viruses from bacteria-containing cultures can present problems because the particle size of giant viruses overlaps with that of smaller bacteria, hence filtration as the only separation method is not possible.In this protocol, a combination of centrifugation, tangential flow filtration, and density-gradient ultracentrifugation is used to concentrate and purify particles of the giant marine virus CroV that infects the heterotrophic flagellate Cafeteria roenbergensis.

Proper citation: Matthias Fischer 2018. Purification of Cafeteria roenbergensis virus particles. protocols.io https://dx.doi.org/10.17504/protocols.io.qz2dx8e Copy   

•   Source:

Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Preparation of trace metal stock solutions for cyanobacteria trace metal mixture (CTMM)

Proper citation: Matthew Sullivan Lab 2015. Primary trace metal stocks. protocols.io https://dx.doi.org/10.17504/protocols.io.c8hzt5 Copy   

•   Source:

Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines our bacteriophage/virus taxonomy analyses. This analysis includes profiles for the average order relative abundance for each site, the phage species relative abundance profiles for each patient, and the relative abundance of specific species between sites. Intermediate files are also included with the publication, and the paths are specified below. Based on the methods from 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 R4: Virome Taxonomy. protocols.io https://dx.doi.org/10.17504/protocols.io.eiabcae Copy   

•   Source:

Authors: Markus G. Weinbauer, Janet M. Rowe, and Steven W. Wilhelm
Group: VERVE Net
Summary: The reduction approach to assess virus production and the prokaryotic mortality by viral lysis stops new infection by reducing total virus abundance (and thus virus–host contacts). This allows for easy enumeration of viruses that originate from lysis of already infected cells due to the decreased abundance of free virus particles. This reoccurrence can be quantified and used to assess production and cell lysis rates. Several modifications of the method are presented and compared. The approaches have great potential for elucidating trends in virus production rates as well as for making generalized estimates of the quantitative effects of viruses on marine microbial communities.

Proper citation: Markus G. Weinbauer, Janet M. Rowe, and Steven W. Wilhelm 2015. Determining rates of virus production in aquatic systems by the virus reduction approach. protocols.io https://dx.doi.org/10.17504/protocols.io.dsp6dm Copy   

•   Source:

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

Proper citation: Bonnie Poulos 2016. Non-Centrifuged Plaque Assay Sample Steps. protocols.io https://dx.doi.org/10.17504/protocols.io.ek2bcye Copy   

•   Source:

Authors: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder
Group: VERVE Net
Summary: For use in "Fingerprinting aquatic virus communities using PFGE"

Proper citation: Ruth-Anne Sandaa, Steven M. Short, and Declan C. Schroeder 2016. Separate different viral genome sizes. protocols.io https://dx.doi.org/10.17504/protocols.io.dy87zv Copy   

•   Source:

Authors: Proro, Melted Mint Forums
Group: VERVE Net
Summary: This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.

Proper citation: Proro, Melted Mint Forums 2015. Autoclave Frankfurter Fiesta. protocols.io https://dx.doi.org/10.17504/protocols.io.ea6bahe Copy   

•   Source:

Authors: Faculty of Medicine Flow Cytometry Facility, U. of Toronto
Group: VERVE Net, Sullivan Lab
Summary: This is a guide to prepare PFA from powder. This is useful for PFA Fixation.

Proper citation: Faculty of Medicine Flow Cytometry Facility, U. of Toronto 2016. Paraformaldehyde (PFA) from Powder. protocols.io https://dx.doi.org/10.17504/protocols.io.c5yy7v Copy   

•   Source:

Authors: John H. Paul and Markus Weinbauer
Group: VERVE Net
Summary: This protocol gives two methods for prophage induction in heterotrophic bacterioplankton; one with no viral reduction and the other with viral reduction (see guidelines).Paul, J. H., and M. Weinbauer. 2010. Detection of lysogeny in marine environments, p. 30–33. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.

Proper citation: John H. Paul and Markus Weinbauer 2015. Prophage Induction in Natural Populations of Heterotrophic Bacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.dn95h5 Copy   

•   Source:

Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in CviRI Purification From XZ-6E Virus Infected NC64A Chlorella.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. CviRI Buffer B. protocols.io https://dx.doi.org/10.17504/protocols.io.esxbefn Copy   

•   Source:

Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: Several methods have been presented by Adams (1959) to determine adsorption kinetics of bacteriophages. One way to measure the adsorption efficiency of cyanophages is to assay for free unadsorbed phages (Suttle and Chan 1993). The principle of this assay is to add a known quantity of viruses to host cells (e.g., at an MOI = 0.01 to 0.1). Over a period of 1 to 2 h, small subsamples of the virus:host solution are removed ca. every 15 min and diluted 100-fold to stop further adsorption. The host is then separated from free viruses by centrifugation, and the number of free viruses remaining in the supernatant determined by plaque or end-point dilution assays. A plot of the abundance of free viruses remaining in solution as a function of time should produce a straight line. The slope of this line is then used to calculate the adsorption rate.This procedure can be adapted for other host–virus systems. The example given is for host BBC1 and cyanophage BBC1-P1 (Suttle and Chan 1993).

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Adsorption of phage to cyanobacteria. protocols.io https://dx.doi.org/10.17504/protocols.io.dq95z5 Copy   

•   Source:

Authors: John Griffith
Group: VERVE Net, Fuhrman Lab

Proper citation: John Griffith 2015. Protocol for Pulsed Field Gel Electrophoresis. protocols.io https://dx.doi.org/10.17504/protocols.io.dmf43m Copy   

•   Source:

Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Preparation of Denaturing Agarose Gel for RNA Analysis.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. 10X MOPS Buffer. protocols.io https://dx.doi.org/10.17504/protocols.io.etgbejw Copy   

•   Source:

Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: Sequence for barcoded oligos for linker amplified libraries. Numbers 1 to 29 were developed at the Tucson Marine Phage Lab dervied from MID 1 to 14 recommended by Roche.

Proper citation: Matthew Sullivan 2016. Barcode Oligos for Linker Amplified DNA. protocols.io https://dx.doi.org/10.17504/protocols.io.ddp25m Copy   

•   Source:

Authors: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith
Group: VERVE Net
Summary: This is a protocol from: Stedman, K. M., K. Porter, and M. L. Dyall-Smith. 2010. Chapter 6: The isolation of viruses infecting Archaea. 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: Kenneth M. Stedman, Kate Porter, and Mike L. Dyall-Smith 2016. Viruses from Hypersaline Waters. protocols.io https://dx.doi.org/10.17504/protocols.io.dph5j5 Copy   

•   Source:

Authors: Kristin Corrier/Nathan VerBerkmoes
Group: VERVE Net, Sullivan Lab
Summary: For use in the "FASP Kit Protocol-ORNL Developed for Bacteriophage"

Proper citation: Kristin Corrier/Nathan VerBerkmoes 2016. Digestion Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.dek3cv Copy   

•   Source:

Authors: DeLong Lab
Group: VERVE Net, Sullivan Lab

Proper citation: DeLong Lab 2015. Proteinase K Solution. protocols.io https://dx.doi.org/10.17504/protocols.io.djf4jm Copy   

•   Source:

Authors: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: For use in "Isolation of cyanophages by plaque assays"

Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Base agar plates. protocols.io https://dx.doi.org/10.17504/protocols.io.dp75rm Copy   

•   Source:

Authors: Priorclave
Group: VERVE Net
Summary: This protocol is part of the VERVE holiday drive to collect exotic off-the-shelf laboratory recipes. More details here.Timing is everything when preparing a large meal.  Unfortunately, for the truly epic holiday meals – like Thanksgiving – there never seems to be enough oven space to ensure everything arrives at the table steaming.  Something has always cooled, collapsed, or coagulated before the turkey is ready to carve.This is where the autoclave comes in:  It’s built to hold loads at around 250 degrees Fahrenheit, and since it subjects them to twice normal atmospheric pressure, it tends to cut cooking times in half. Autoclave cook-time for a small to mid-sized turkey should be less than 2 hours.Wanna impress the in-laws this year?  Bring home your favorite tabletop food-grade autoclave (not your Priorclave, though; those are research-grade autoclaves!) and put it to use on the big day.

Proper citation: Priorclave 2016. Thanksgiving Dinner Autoclave Style. protocols.io https://dx.doi.org/10.17504/protocols.io.ea9bah6 Copy   

•   Source:

Authors: Forest Rohwer
Group: VERVE Net, Sullivan Lab
Summary: This protocol is based on RT Noble and JA Fuhrman (1998) Aquatic Microbial Ecology 12:113-118: Use of SYBR Green I for rapid epifluorescence counts of marine viruses and bacteria.

Proper citation: Forest Rohwer 2016. SYBR Green or Gold Staining. protocols.io https://dx.doi.org/10.17504/protocols.io.c7sznd Copy   

•   Source: