So cool that you did Ben and Nick’s measles paper! Ben and I have talked about how interesting it would be to put the influenza glycoproteins into the measles genome and do the subsequent mutagenesis… But Dr. Palese said he didn’t want to go to jail.
I would like to submit a listener pick for consideration. In this video Bill Gates discusses why the government should be funding initiatives to prepare for pandemic viral outbreaks (that spread more readily than ebola) https://www.youtube.com/watch?v=9AEMKudv5p0
I am a twix groupie. I love and listen to every minute. I have one minor request, at least for TWIV. When you dive deeply into a complicated study, maybe you could give introductory and concluding sentences meant for the non-PhD’s in the audience. Alan would be great at that.
Wink (not-a-wonk) Weinberg
Limits to variability
For Dr. Condit to deal with some challenges:
Compute Earth’s Magnetic Field Values http://www.ngdc.noaa.gov/geomag/magfield.shtml
Pollen Allergy Forecast for Gainesville, FL (32601)
The number of variants is constrained by the structure of the variants and the structure of the domain in which they operate. For viruses, the domain in which they operate includes aspects of infectivity such as transmissibility, receptors and host defences. The measles virus in its configuration must effectively elude unvaccinated host defences while maintaining infectivity and transmissibility; one or another would be compromised by variation: hence the configuration is so strongly conserved.
The structure of the variants can be constraining if too big an evolutionary jump to a new variant is needed. That’s why unicorns and pigs with wings are so rare.
Loved your discussion on episode 340 of the recent paper looking at constraints on measles virus mutation. It reminded me of a post I wrote back in February looking at an argument that cropped up from the anti-vaccination side of things. With the measles outbreak at Disneyland spreading quickly, they blamed first the vaccine because it “didn’t work”, then shifted to blaming the vaccinated for spreading vaccine-strain measles. Fortunately, genetic analysis had already been done and identified the genotype responsible for the outbreak. In my post, I tried to distill info on genotypes, serotypes and epitopes into something a layperson could grasp. If you have time, give it a look and let me know what I messed up. I added a link to the measles paper you discussed.
P.S. In Boston, it’s currently 68F/20C with a chance of showers and forecast for continued slightly below-average temps ahead.
Hello, TWiV team!
Regarding the measles paper, were the resulting mutant proteins examined to ensure that the inserts were translated into amino acids and integrated? It seems possible to me that the insertions may have caused a fold in the viral RNA structure that could have affected translation. A review of the resulting amino acid sequences would rule out any such reaction. I bring up this question because a couple years of playing around with RNA secondary structure simulations has taught me that some sequences will tolerate very little variation before an unwanted fold forms or vice-versa.
As always, I appreciate the time and work you guys put into the show. Keep it up!
I’m sitting here listening to twiv 340 and Rich’s enthusiastic endorsement of Northern blots for RNA analysis (re: twiv 339). Bravo!
But as I listened to twiv 339, and then Rich’s response, I found myself considering a combination of PCR-based quantification with an even more retro technique for RNA sizing by running sucrose gradients (that may take some explanation for at least some of your listeners). The RNA in each fraction could then be assayed by qRTPCR, using primer sets targeted to any particular viral genome region. Having liquid samples that can be subdivided for multiple analyses often is easier than reprobing blots. And if you do it this way, you don’t need radioisotopes.
It’s partly cloudy and 74*, the dew point is 56°, and we may get some more severe storms today in Hershey.
Keep on twivvin’,
David J. Spector, Ph. D
Professor Emeritus of Microbiology and Immunology
Penn State Hershey
Just heard the recent discussion on lab Safety and reporting. I thought Alan was going to steer the discussion towards the NASA reporting system for aviation accidents. I thought that it would be a good model system especially because reporting helps to reduce the chance of federal involvement. Just thought this might help further the conversation.
All is well here in the Charm City at 72F with a possibility of 92F and some T-Storm. Love the show and that you make it accessible to a non-technical type.
ASRS – Aviation Safety Reporting System
I have to disagree with Alan about the USA Today article. If this were an isolated article, I might agree that this is good reporting with a sensationalist spin added after the fact. But the reporters at USA Today knowingly went looking for news that they could put out as sensationalist, yellow, journalism.
How do I know this? Not just because USA Today’s headlines often sound like clickbait. This is the latest in a series of sensationalist articles on biosafety, mostly written by Alison Young. They have a page for the stories released over the last year: http://www.usatoday.com/topic/9ee9e5de-b702-4fbc-9e5d-1b595adcf938/biolabs/ Now most of those are sub-articles from the article discussed last week, but plenty are earlier, and USA today’s sensationalist coverage goes back even before that. Many of those articles are built around finding incidents and exaggerating (or completely making up) the danger that they posed to the general public. So I have no doubt that the editor and journalists involved—if they know anything about what they’re reporting on—went looking for an excuse for fear mongering.
Frankly I have an image of USA Today’s newsroom as run by a real world J. Jonah Jameson—for those who don’t know, that’s the fictional newspaper editor who is constantly looking for some scrap of evidence that would cast Spiderman in a bad light. Instead of turning Spiderman from hero to villain, USA Today is villainizing scientists trying to limit disease. And since the staff at USA Today isn’t fictional, they don’t even get to be characters we love to hate.
And we can’t excuse USA Today as not knowing better, not being specialist enough, or not having enough voices speaking out from the other side. Other media companies can take a measured look at biosafety incidents, and don’t try to pretend that scientists are about to kill every last one of us.
I was especially impressed with Alan’s comparison of ethyl and methyl alcohols to methyl and ethyl mercury in the group’s short discussion about thimerosal. I also was not aware that the reason thimerosal is still used is to prevent contents contamination in multiple-use containers of vaccine. All this is easily understood by us lay folks and easy to pass on. Thanks for those two insights.
Love the podcast guys, please keep ’em coming! Thought you might find our paper of interest.
H. Benjamin Larman, Ph.D.
Johns Hopkins School of Medicine
Hello Doctors TWiV,
I’ve been listening to your show since episode 3 was posted to itunes way back when, and I’d like to start by saying thank you for all the work you all do to get so much interesting information out to the public in a (usually) easy-ish to understand for the layman way.
I recall hearing on this week’s episode (339) Vincent and Alan joking about a device that would tell you what viruses you currently have in your body, when I came upon this article through fark.com.
That link is to a media story that links to this Science Magazine article titled
Comprehensive serological profiling of human populations using a synthetic human virome
I’m no virologist and I don’t understand everything in the structured abstract, but it seems like it could be used to do exactly what you joked about. Run the test every day, and whatever shows up that hasn’t been seen before would be your viruses for the day. Is ~25 bucks a day worth it to know?
Obviously it wouldn’t be quite that simple, but you get the picture. What do you think about this test? Is it really as accurate as the mnn.com article made it out to be?
Anyway, as I said, long-time listener to all the podcasts. Thanks again for all the work you do in making the world a smarter place.
A possible pick for the super Twiv Gang.
The Kardashian Index: a measure of discrepant social media profile for scientists.
by Neil Hall
In the era of social media there are now many different ways that a scientist can build their public profile; the publication of high-quality scientific papers being just one. While social media is a valuable tool for outreach and the sharing of ideas, there is a danger that this form of communication is gaining too high a value and that we are losing sight of key metrics of scientific value, such as citation indices. To help quantify this, I propose the ‘Kardashian Index’, a measure of discrepancy between a scientist’s social media profile and publication record based on the direct comparison of numbers of citations and Twitter followers.
The author does not include brilliant, fascinating, educational podcasts in his data.
Near lovely Buda Texas it is muggy at 70F with 10 days of scattered showers and thunder bumpers forecast. The cattle are lying down this morning.
Hi twiv team!
I am Giann, a future MS Biology student from the Philippines. I’ve been listening to your podcast for about 6 months now and I’ve been inspired by much of what you discuss here.
I recently finished my second degree (BS Biology) from the university and am applying for grad school. I am hoping to pursue virology but resources and faculty from my university seem to be limiting. At times, I am discouraged by some PhD students to pursue virology due to the aforementioned obstacles but I don’t see myself settling for anything less.
I honestly do not know what to do to get into virology. I figured that making a thesis on virology would be a good start but it seems difficult to even gather the materials for it. At times I hear about the works of undergrad students from developed countries and it frustrates me that I cannot do anything remotely similar to what they do. Of course I will not let these hinder my becoming a virologist.
To cut things short, my questions are:
What do I do to get into a great virology program? Are there means to make the program available to an “average to above average” but very driven student?
>> What got me into virology was Prof. Racaniello’s youtube series on virology which means I blame him for getting me into this limbo. Just kidding. But his videos and the podcast really did bring me into virology.<<
It is now 36C here in Quezon City, Philippines. With an 80% chance of precipitation and winds of 6 kmph.
I came across the topic of using bacteriophages as an alternative to conventional anti-bacterial therapies as a tool in the fight against multi-resistant bacterial infections.
I was wondering what you guys know and think about this approach. What would you forsee are the hurdles that need to be overcome to get this FDA approved? And is this a good idea in the first place?
And of-course a very big thank you for TWIV!! It goes without saying, I am a big fan 🙂
PS: Here in Germany the weather is currently rather wet and cold for this time of year.
Disease puts rare migratory parrot on verge of extinction
JUNE 01, 2015 12:00AM
The last wild population of an Australian parrot on the brink of
extinction has been hit with a potentially deadly disease, leading to
a disastrous breeding season and fears the orange-bellied parrots’
annual migration from Tasmania to Victoria and South Australia this
winter could be its last.
The Threatened Species Commissioner, Gregory Andrews, confirmed
yesterday that he had been briefed on an outbreak of beak and feather
disease in the only wild population of orange-bellied parrots, already
categorised as one of the world’s rarest and most endangered species.
Its wild population is believed to be as few as 50 birds, with a
further 345 in a captive breeding program.
. . .
# # #
A virus causes Psittacine Beak and Feather Disease (PBFD).
# # #
BTW, thank you for reading my letter on the TWIV of 5/30. When I
wrote that wild birds were not found to be the cause of influenza in
poultry, I meant in particular this current outbreak in the Midwest.
Of course, migratory birds are in general the usual suspects.
Thank you again for your wonderful shows — with TWIV as the jewel in the crown!
The hurdle to educating the public about science and genetically modified organisms is higher than you think.
As a full time Mom, I’m baffled by the dramatic increase in food fear and pseudoscience among my cohort. The level of time, effort, and constant near panic put towards GMOs, processing, toxins, allergens, dyes, chemicals etc is very sad to observe.
Anyway, I think my pic(ture) of the week speaks volumes to the depth of the lack of basic science knowledge out there… Non-GMO table salt.