TWiV 151: Dear TWiVers

viral mailHosts: Vincent Racaniello, Alan Dove, and Rich Condit

Vincent, Alan, and Rich review questions and comments from TWiV listeners

Click the arrow above to play, or right-click to download TWiV 151 (49 MB .mp3, 81 minutes).

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Links for this episode:

Weekly Science Picks

Alan – Aurora Australis from space
Vincent –
Science360 Radio
Rich – 
Ghost Productions (demo and website)

Listener Pick of the Week

SophieBacteria by Jonathan Coulton

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 150: Contaminated

pXMRVHosts: Vincent RacanielloRich Condit, and Dickson Despommier

Vincent, Dickson, and Rich meant to do an all-email episode, but first they review results of the Blood XMRV Scientific Research Working Group, and partial retraction of the paper associating XMRV with chronic fatigue syndrome.

With this episode TWiV is three years old.

Click the arrow above to play, or right-click to download TWiV 150 (56 MB .mp3, 93 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

Weekly Science Picks

Dickson – The Tree of Life
Vincent –
When do you fact-check article content with sources? (take as directed)
Rich –
io9

Listener Pick of the Week

LuisNIH videocasting and podcasting

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 146: Draco’s potion

dracoHosts: Vincent RacanielloRich Condit, and Abbie Smith

Vincent, Rich, and Abbie review a broad spectrum antiviral protein, and selective pressure applied by a failed HIV-1 vaccine.

Click the arrow above to play, or right-click to download TWiV 146 (78 MB .mp3, 107 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

Weekly Science Picks

Vincent – Hypothetical Risk: Cambridge City Council’s Hearings on Recombinant DNA Research
Rich –
Z Corporation 3-D printer (YouTube)

Listener Pick of the Week

JimDo-it-yourself DNA extraction (Citizen Scientist Quarterly)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 144: HIV gets the (zinc) finger

zinc finger nucleaseHosts: Vincent Racaniello, Rich Condit, and Alan Dove

Vincent, Rich, and Alan discuss live blogging of scientific meetings, the current outbreak of Hendra virus is Australia, and using zinc finger nucleases to make HIV-resistant CD4 cells.

Click the arrow above to play, or right-click to download TWiV 144 (75 MB .mp3, 104 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

Weekly Science Picks

Alan – Bugscope
Rich –
Vaccine adverse events: Causal or coincidental? (Lancet)
Vincent – West Nile Story by Dickson Despommier (Kindle edition)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 140: An aptitude for microbicides

cd4 aptamer

Hosts: Vincent Racaniello, Alan Dove, Rich Condit, and Judy Lieberman

Vincent, Alan, Rich, and Judy Lieberman review the use of CD4 aptamer-siRNA chimeras to inhibit HIV transmission.

Click the arrow above to play, or right-click to download TWiV #140 (110 MB .mp3, 92 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

Weekly Science Picks

Alan – Inside insides
Rich – Rock stars of science
Vincent – A new open-access journal, and Francis Collins on NIH budget

Listener Pick of the Week

Kathy – Scientists and musicians compare notes (NPR)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv, or call them in to 908-312-0760. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 119: Science and journalism with David Tuller

science journalismHosts: Vincent Racaniello and David Tuller

On episode #119 of the podcast This Week in Virology, Vincent and journalist David Tuller converse about the state of science reporting by the press.

Click the arrow above to play, or right-click to download TWiV #119 (43 MB .mp3, 60 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with the Microbeworld app.

Links for this episode:

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 110: CSI virology

Alan DoveHosts: Vincent Racaniello, Dickson DespommierAlan Dove, and Rich Condit

On episode #110 of the podcast This Week in Virology, Vincent, Alan, Rich, and Dickson discuss bacteria that can utilize arsenic in place of phosphorus, the passing of Frank Fenner, polio outbreak in The Congo, solving criminal cases of HIV transmission, and classifying viruses by capsid structure.

Click the arrow above to play, or right-click to download TWiV #110 (68 MB .mp3, 93 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio.

Links for this episode:

Weekly Science Picks

Dickson – CDC’s West Nile virus case count for 2010
Rich –
The red bees of Red Hook
Alan – Arsenic-based life at XKCD
Vincent –
PLoS iPad app

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 108: Barking up the right Tre

twivHosts: Vincent Racaniello, Alan Dove, Rich Condit, and Saul Silverstein

On episode #108 of the podcast This Week in Virology, Vincent, Alan, Rich, and Saul review the evolution of HIV-1 specific recombinases, and down-regulation of a host microRNA by a viral noncoding RNA.

Click the arrow above to play, or right-click to download TWiV #108 (64 MB .mp3, 89 minutes).

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio.

Links for this episode:

Weekly Science Picks

Rich – Where cinema and biology meet
Alan – Qiagen iApp
Vincent –
Ask a biologist

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

TWiV 92: Live at ASV in Bozeman

Hosts: Vincent Racaniello, Rich Condit, Karla Kirkegaard, and Marilyn Roosinck

On episode #92 of the podcast This Week in Virology, Vincent, Rich, Karla, and Marilyn recorded TWiV at the 29th Annual Meeting of the American Society for Virology in Bozeman, where they discussed plant viruses and how they make plants resistant to adverse conditions, and identification of dominant negative drug targets.

Click the arrow above to play, or right-click to download TWiV #92 (42 MB .mp3, 57 minutes)

Subscribe to TWiV (free) in iTunes , at the Zune Marketplace, by the RSS feed, or by email, or listen on your mobile device with Stitcher Radio.

Links for this episode:

Weekly Science Picks

Marilyn – Viruses in the faecal microbiota of monozygotic twins and their mothers (Nature)
Rich –
The Known Universe by the American Museum of Natural History
Vincent – The Red Queen by Matt Ridley (thanks, Jesper!)

Send your virology questions and comments (email or mp3 file) to twiv@microbe.tv or leave voicemail at Skype: twivpodcast. You can also post articles that you would like us to discuss at microbeworld.org and tag them with twiv.

Virology toolbox: the western blot

Readers of virology blog often request explanations of specific experimental techniques. Methods such as complement fixation, deep sequencing, ELISA, PCR and many others are frequently mentioned on this blog without discussion. To do so would interrupt the scientific discourse and make for lengthly posts. To remedy this shortcoming, I have added a new tab to the first page of virology blog called Virology Toolbox. This page will be populated with explanations of experimental techniques used for the study of viruses. Today’s technique is the western blot.

Western blot analysis (also known as immunoblotting) is used to detect a specific protein in a cell, tissue, organ, or body fluid. The technique depends on the reaction of an antibody with a protein that is immobilized on a thin membrane (click the figure for a larger version). The sample is solubilized with detergent, and the proteins are then separated by electrophoresis in a polyacrylamide gel. After electrophoresis, the gel is placed next to a thin, synthetic membrane that has a strong affinity for proteins. In the figure, the gel and membrane are placed between sheets of absorbent paper in a blotting tank. This arrangement allows buffer to flow across the gel and through the thin membrane. As a result, the proteins in the gel are transferred to the membrane by capillary action. Transfer of the proteins to the membrane may also be accomplished by an electrical current.

After the transfer step, the membrane is incubated with an antibody to a specific protein. This antibody may be produced in an experimental animal such as a mouse or rabbit, or in cells as a monoclonal antibody. The antibody may be coupled to an enzyme which can then be used to detect the antibody on the membrane. In the example shown, the antibody is coupled to horseradish peroxidase. The membrane is incubated with a substrate that is converted to a luminescent compound after reaction with this enzyme.  A sheet of X-ray film is then placed next to the membrane, which allows visualization of individual proteins. In a variation of the technique, an unlabeled first antibody is used to bind the protein on the membrane, and a second antibody, directed against the first antibody, is used for detection.

The main advantage of western analysis is that it does not require isotopic labeling of proteins and can be used with tissues and organs, as well as cultured cells.

A variation of the western blot is used to identify antibodies to human immunodeficiency virus in clinical specimens and donated blood. Viral proteins are fractionated by electrophoresis and transferred to a membrane as describe above. The membrane is then incubated with the clinical sample. If antibodies against HIV are present, they will react with one or more of the viral proteins on the membrane. Such an assay is being used to estimate the extent of infection with the retrovirus XMRV in the general population.

Note that the w in western blot is not capitalized. The n of northern analysis (a method in which RNA is detected on a thin membrane) is also lower case. However, Southern analysis deserves a capital S – it’s the last name of Edwin Southern, who in 1975 developed the technique for detecting DNA immobilized on a membrane.