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Authors: Jennifer Brum
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This protocol describes how to adsorb viruses onto TEM (transmission electron microscopy) grids. The sample is allowed to sit on a hydrophilic grid and viruses adsorb onto the surface of the grid. This technique is generally used for viral lysates with high concentrations of viruses. For natural samples, use the protocol “Quantitatively Depositing Viruses onto TEM Grids using an Airfuge”.Note: If purification of the viruses is necessary, refer to Ackermann and Heldal (2010) for various options.
Proper citation: Jennifer Brum 2016. Adsorbing Viruses on TEM Grids. protocols.io dx.doi.org/10.17504/protocols.io.dar2d5 Copy
Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Proper citation: Bonnie Poulos 2016. Transcriptomics During One-Step Growth Curves for Cellulophaga Phages. protocols.io dx.doi.org/10.17504/protocols.io.ek4bcyw Copy
Authors: Li Deng
Group: VERVE Net, Sullivan Lab
Summary: Case 2: Fix samples. Use this protocol when long term storage of slide is required.For when you can count your samples in a few days, see Case 1.
Proper citation: Li Deng 2016. SYBR Gold Staining for Viral Enumeration (Case 2). protocols.io dx.doi.org/10.17504/protocols.io.c7fzjm Copy
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 assyays"
Proper citation: Mathias Middelboe, Amy M. Chan, and Sif K. Bertelsen 2016. Top agarose. protocols.io dx.doi.org/10.17504/protocols.io.dqh5t5 Copy
Authors: HANNIGAN GD, GRICE EA, ET AL.
Group: VERVE Net, Club Grice
Summary: This protocol outlines our alpha diversity analyses of the virome (from PHACCS) and whole metagenome (from MetaPhlan OTU table). We start by comparing the virome and whole metagenome alpha diversity values, and then look at the differences in virome and whole metagenome diversity between skin sites. 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 R5: Virome Alpha Diversity. protocols.io dx.doi.org/10.17504/protocols.io.eimbcc6 Copy
Authors: Nick Tang
Group: VERVE Net, Upton-Lab
Summary: Viral Bioinformatic Resource CentreProvide databases of viral genomic information. Please check the Organisms menu to see which viruses we support: we’re now focusing on large DNA viruses
The VOCs (Virus Orthologous Clusters) database is at the heart of our system.
The database links directly to integrated tools for comparative analyses.
VOCs sorts genes into ortholog clusters (e.g. RNA polymerase) to simplify data retrieval.
Provide easy access to the genes, gene families, and genomes of the different virus families. via a unique series of powerful Java tools that support multiple computer platforms (see VBRC Tools menu).
design and build software to tackle specific bioinformatics/virology problems, often in collaboration with virologists.
Rally the research community to provide expert curation of these viral genomes by: Adding value to GenBank sequences through enhancing and updating genome annotations
Linking to research reviews/papers for the research community.
Collaborate with researchers to help on specific bioinformatics problems, e.g. Custom searches of the databases
Building new features into our tools
Help with genome annotation
Proper citation: Nick Tang 2016. VBRC Base By Base: Search for a sequence motif, either exact (regular expression search) or inexact (fuzzy motif search). protocols.io dx.doi.org/10.17504/protocols.io.eczbax6 Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Summary: For use in CviJI Purification From IL-3A Virus Infected NC64A Chlorella.
Proper citation: David Dunigan and Irina Agarkova 2016. CviJI Buffer A. protocols.io dx.doi.org/10.17504/protocols.io.esibece Copy
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. Centrifuged Plaque Assay Sample Steps. protocols.io dx.doi.org/10.17504/protocols.io.dep3dm Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Proper citation: Matthew Sullivan 2016. Titration of AmPure XP Beads for Removal of Fragments . protocols.io dx.doi.org/10.17504/protocols.io.c52y8d Copy
Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: For One-step growth curves for Cellulophaga phages protocol and Transcriptomics During One-Step Growth Curves for Cellulophaga Phages protocol.
Proper citation: Matthew Sullivan 2016. Cellulophaga growth reading. protocols.io dx.doi.org/10.17504/protocols.io.dpa5id Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: 10g/L Fe Stock Solution for Iron Chloride Precipitation of Viruses from Seawater Protocol.
Proper citation: Matthew Sullivan Lab 2015. 10g/L Fe Stock Solution. protocols.io dx.doi.org/10.17504/protocols.io.c2zyf5 Copy
Authors: André M. Comeau and Rachel T. Noble
Group: VERVE Net, Suttle Laboratory of Marine Molecular Microbiology and Virology
Summary: The steps describe how to prepare each virus concentrate. There are multiple options for many of the steps; in the case where there is more than one option they are noted in annotations.
Proper citation: André M. Comeau and Rachel T. Noble 2016. Concentration of viruses and preparation of FLVs for tracer assays. protocols.io dx.doi.org/10.17504/protocols.io.dzv765 Copy
Authors: Rex Malmstrom
Group: VERVE Net, Sullivan Lab
Summary: This is a storage solution that stabilizes and protectsRNA while inactivating RNase
Proper citation: Rex Malmstrom 2015. RNAlater Recipe. protocols.io dx.doi.org/10.17504/protocols.io.c56y9d Copy
Authors: Joshua Weitz
Group: VERVE Net
Summary: BiMat: a MATLAB package to facilitate the analysis of
bipartite networks.
Extensive documentation, code, and worked examples available on:
http://bimat.github.ioThe datasets included with the package include phage-bacterai infection networks.
Proper citation: Joshua Weitz 2016. BiMat: a MATLAB package to facilitate the analysis of bipartite networks. protocols.io dx.doi.org/10.17504/protocols.io.fajbicn Copy
Authors: David Dunigan and Irina Agarkova
Group: VERVE Net
Proper citation: David Dunigan and Irina Agarkova 2016. Dot Blot Preparation. protocols.io dx.doi.org/10.17504/protocols.io.etibeke Copy
Authors: Carolina Cadena
Group: VERVE Net
Summary: This protocol is based on the study done by two members of the Biological and Agricultural Engineering department at UC Davis which analyzes the ability of infrared spectroscopy to detect fungal infections in almonds. The methods section of this article was adapted to fit the protocols.io format.
Source: “Detection of fungal infection in almond kernels using near-infrared reflectance spectroscopy”. Pei-Shih Liang, David C. Slaughter, Alejandro Ortega-Beltran, Themis J. Michailides. Biosystems Engineering, Volume 137, September 2015, Pages 64–72
Proper citation: Carolina Cadena 2016. Detecting Fungal Infections in Almonds. protocols.io dx.doi.org/10.17504/protocols.io.etnbeme Copy
Authors: Jonathan King
Group: VERVE Net, Sullivan Lab
Summary: This mixture is used in the CsCl Step Gradient to Purify Phage Protocol
Proper citation: Jonathan King 2016. CsCl Step Gradient Buffer. protocols.io dx.doi.org/10.17504/protocols.io.dmj44m Copy
Authors: Benjamin Bolduc
Group: VERVE Net, Sullivan Lab, iVirus
Summary: A collection of protocols designed to guide the user in processing a viral metagenome from raw sequence data to assembly, and subsequent analysis. The user uses actual reads from Ocean Sampling Day (2014) and processes them entirely within Cyverse, a NSF-supported cyberinfrastructure.
Proper citation: Benjamin Bolduc 2019. Applying vContact to Viral Sequences and Visualizing the Output (Cyverse). protocols.io dx.doi.org/10.17504/protocols.io.x5xfq7n Copy
Authors: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John
Group: VERVE Net, Sullivan Lab
Summary: Purpose: This method for the enumeration of aquatic viruses is a low-cost alternative to the commonly used filter-mount method. Briefly, fluorescently-stained samples are wetmounted directly onto slides for epifluorescence microscopy after an optional chemical flocculation concentration step used for samples with anticipated virus concentrations of 7 viruses mL-1 (samples with >5×107 viruses mL-1 do not require this concentration step prior to analysis). Virus concentration in the wet-mounted sample is determined from the ratio of viruses to microsphere beads, which are added at a known concentration. This wet-mount method for enumerating viruses is significantly less expensive than the filter-mount method (i.e., the cost of microsphere beads per sample is ~500-fold lower than the cost of one filter per sample), and is appropriate for rapid, precise and accurate enumeration of aquatic viruses over a wide range of viral concentrations encountered in field and laboratory samples. The only limitation of this method is that samples with virus concentrations ≤1×106 viruses mL-1 cannot be enumerated, as the abundance of viruses is too low for efficient enumeration.Figure 1. Overview of the wet-mount method for enumeration of aquatic viruses.
Proper citation: B.R. Cunningham, J.R. Brum, S.M. Schwenck, M.B. Sullivan, S.G. John 2016. Wet-mount Method for Enumeration of Aquatic Viruses. protocols.io dx.doi.org/10.17504/protocols.io.c8pzvm Copy
Authors: Matthew Sullivan Lab
Group: VERVE Net, Sullivan Lab
Summary: Supplement to seawater for growth of cyanobacteria.
Proper citation: Matthew Sullivan Lab 2015. 0.5M NH4Cl. protocols.io dx.doi.org/10.17504/protocols.io.c77zrm Copy
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