TWiV 249 letters

Suzanne writes:

That is a cool idea! Instead of a heart, though, it might be neat to see them leave a stamp that would last a little while with the vaccine’s initials. My kids’ doctors (or the nurse or PA, actually) would write them on the bandaids the first few times when there were multiple shots so we’d have an idea which was which in case there was any swelling or local allergic reactions in the following few hours. But even though my kids were infants at the time they were pretty good at getting rid of the bandaids.

Ann writes:

Hi TWIV gang,

I was bummed to miss your session at Harvard last month, Episode #244. Experiments kept my too busy.

I just wanted to request that you update the link for our student group ‘Science in the News’, Jeff’s pick of the week. We still have some confusing problems with re-directing to the old/inactive website. So please post this link to our NEW and active website: sitn.hms.harvard.edu

Thanks!

Ann

PhD Candidate

Harvard Program in Virology

Lee Gehrke Laboratory

Stefan writes:

Dear TWIV team,

I was just listening to TWIV 247 and I really like the idea of a TWIV index and summary for each episode. I extensively integrate TWIV episodes in my classes and I find it more and more difficult to remember in which episode you were talking about certain issues. Funny titles like Today’s Weather in Virology work in my short term memory but don’t last too long.

Since this is quite a task for one person how about putting this out as a project for your TWIV listeners. With 10,000 followers a week you can probably get this done between episodes 😉 Maybe a public dropbox folder with template file would work or a TWIV wiki (I am sure there are tons of other possibilities). As Kathy suggested this can also include keywords, long forgotten ideas, as well as show topics and guests.

Keep up the great work and special greetings to Kathy, hearing her on TWIV reminds me of our SWIG meetings and makes me feel home. Go Blue …

Best from Lübeck Germany (the capital of marzipan) …

Stefan

—

Stefan Taube

Assistant Professor

UNIVERSITY OF LUEBECK

Institute of Virology and Cell Biology

Adam writes:

Hi Dr. Racaniello,

Here is a recently published paper I thought you and TWIV fans would find interesting. It is about statistically estimating the number of (and cost to identify) all unknown mammal viruses based on viral sampling of the Indian Flying Fox (Pteropus giganteus). Further, it discusses the big picture impact and cost/benefit of such an undertaking. While it likely isn’t enough to have a show on, I thought it may be interesting to mention!

http://mbio.asm.org/content/4/5/e00598-13

As always, keep up the good work!

Adam

1st year student in the Molecular and Cellular Biology PhD/MS Epidemiology at the University of Washington and the Fred Hutchinson Cancer Research Center

Jennie writes:

Of course you know about this sequencing of all mammalian viruses – starting with flying foxes……but just in case you don’t: The Scientist:

http://www.the-scientist.com/?articles.view/articleNo/37327/title/How-Many-Mammalian-Viruses-/

Yours with warmest regards

Jennie BSN RN

Oneonta, NY

Jenn writes:

Greetings all,

Love the show (and twip, haven’t gotten around to checking out twim yet, as this is a fairly recent discovery for me).

Forgive me if this has already been addressed, as I am only on episode 27, but I remember reading a book called “Ebola” a few years back, about an ebola outbreak at the Yambuku mission hospital in Africa. A man came in with symptoms they thought indicated malaria, and received an injection of chloroquine. This man later came down with ebola Zaire.

http://www.stanford.edu/group/virus/filo/eboz.html

Many patients were given injections that day with the same needle, and this was believed to have caused the rapid spread of the disease. Undoubtedly, many of the injections were likely chloroquine.

My question is, as this seemed to be a particularly nasty outbreak (not that I can think of a “nice” ebola outbreak), are the chloroquine doses administered for malaria not high enough to have an effect on ebola, or does it need to be administered intravenously for an anti-ebola effect possibly?

Many thanks and keep up the great work!

Jenn

PS

I forgot to ask about “Super-Rabies.”

Is this article for real, or has NatGeo resorted to junk-science as well?

http://news.nationalgeographic.com/news/2009/05/090504-rabies-evolution_2.html

Jacob writes:

Hi all,

I am interested to hear the opinions of the TWiV team about the new section that Nature have decided to include in their journals. It is an “Extended Data” section, which allows authors to present additional data in the online and PDF versions as if it were a results section, rather than isolated in the supplementary information.

http://www.nature.com/news/announcement-nature-papers-enhanced-1.13125?WT.ec_id=NATURE-20130606

Thanks,

Jacob.

Jenn writes:

Hello Twiv Team,

I know this is probably not a huge worry, but do you know if anyone has looked at a possible link between cormorant fishing (the use of cormorants to catch fish, which are half-swallowed by the birds, but prevented from going all the way down the by a rope tied around the base of the bird’s throat – which are then brought back up by the fishermen in China and Japan) and H5N1?

I realize farms and poultry in live markets are probably a far greater likelihood of disease transmission, but considering some of these fish are actually shipped to different parts of China for consumption, is this a worry? I do remember you saying in at least a couple of episodes that the flu can live for day on bank notes, especially if they contain mucous.

Thank you for all the great podcasts!

Jenn

P.S. I know they’re a bit out of date now, but I don’t think I’ve ever heard you pick “Men Against Death” or any of Berton Roueché’s works. While they may be a smidge antiquated, they’re still incredibly interesting from a historical perspective, and I think that most of your listeners are smart enough to realize that science is ever-evolving, and a book published 50-80 years ago might be a bit off on some of the scientific facts.

Todd writes:

I have have been a Twiv fan since hearing Vincent and Dick on the Futures in Biotech podcast.

I immediately downloaded all the past episodes and I am current with Twiv and a little behind with Twip and Twim.

Twiv and a 2 other science and skeptical podcasts get priority, while other are pushed to “my queue” for any time I’m driving or working around the house. I look forward to each weeks discussions and always listen to the end!

I’m so grateful that Rich decided to stop emailing from his bicycle and pull up a co-host chair! The additions of Alan, Rich and Kathy have done nothing but fortify my appreciation of the the podcast while topping off the Twix brain trust.

“Trust” is an essential term here and I’m sure I speak for thousands when I tell you that I thank you all for your diligence and the time you donate to our knowledge and good health!

Over time,”the picks” have become one of my favorite parts of the show, and as weather geek, I pay special attention to the meteorological stuff.

Alan’s Wind Map pick is a useful, as well as mesmerizing, daily destination for me, as well as 2 others.

http://weatherspark.com/ is a customizable weather graph showing past, present a future values. For me, becoming familiar with this site gives me the “weather at a glance” so I no longer need to scroll the pages of hourly forecasts on more popular weather sites. In my browser at least, I can spin the mouse scroll wheel to expand or contract the graph and then drag the graph along to find a particular date and time to focus on. I tend to close the site with the radar so I can get more data, and use my second pick for radar.

It is http://www.imap.tv/ . This is a zoom-able satellite map, with an array of layers on the right that you can add or subtract to let you find the type of info you are interested in. It also has icons for many storm-chasers that are live streaming as they roll along. I have seen the Imap logo flash on CNN’s coverage many times in the past month or two.

It’s currently 55F here in Northern Colorado at 8:00am on Sunday. Several days of temps getting in the high 90s and possibly hitting 100F are on the way.

Cheers, Todd.

Kevin writes:

Hi Twivsters,

I’m a graduate student studying innate immune recognition at Harvard, and I wanted to chime in on your discussion from TWiV 236 – I think you guys may have overlooked the most parsimonious explanation.

I will preface by saying that we don’t fully understand what it is about nucleic acids that make them good ligands for innate immune receptors, so it is entirely possible that some difference in secondary structure of the RNA is leading to the difference in response. It is also entirely plausible that selective pressure would push the influenza genome to be as unrecognizable as possible. However, the way we usually think about innate recognition is that it’s directed against non-specific patterns, things like double stranded RNA, or RNAs with un-capped 5′ tri-phosphate. Our innate recognition would rapidly be rendered useless if viruses could just use different codons (and therefore different secondary structured genomes) for the same proteins.

So, I wonder if the best explanation is just that the virus is just slower to kill the host. Wild type PR8 likely generates a robust adaptive memory response, but the mice die before that memory response is useful. Since the deoptimized viruses have all the same proteins, and are presumably equally able to infect cells, they may generate an equivalent immune response to the WT, without being as lethal.

A related possibility is that an infected cell is making the equivalent number of viral genomes in a cell, but less able to release those genomes due to a lack of HA and NA. The cytoplasmic RNA sensors don’t just detect in-coming genomes, they can detect replication intermediates as well. Maybe it has nothing to do with the structure of the RNA, but rather the amount of viral RNA per infected cell.

-Kevin

PS – There may be an indirect way to test if it is indeed the secondary structure of the RNA. If the secondary structure of the RNA was important, presumably the WT influenza would have been selected for the least visible. If you mutated the codons without selecting for low-availability tRNAs, you should see an increase in immune recognition, without necessarily slowing down the production of protein.

Hannah writes:

Dear TWiV,

I know you try to avoid getting stuck in an influenza rut, but you should consider doing this paper anyway, because it’s quite neat.

http://www.nature.com/doifinder/10.1038/nature12202

Nicole writes:

Dear Twiv team,

I very much enjoy your podcast and like most others am currently working my way through the archives. When I saw the much hyped news story about the possible discovery of woolly mammoth blood I was listening to TWIV #100 where the timetree app was Alan’s pick and your discussion of how viruses are not included in this tree of life. I was wondering if this discovery actually was blood and some was preserved (it is hard to imagine any DNA or RNA remains), how would you use this sample to fill in knowledge gaps in viral evolution? What could you do with a limited amount of a well-preserved sample?

http://news.nationalgeographic.com/news/2013/06/130601-woolly-mammoth-blood-russia-science-extinct-species-deextinction/

Sincerely,

Nicole

Jing writes:

Dear TWIV hosts,

I’m a junior postdoc joining my current lab in summer 2012, by the end of last year I made an important discovery and if I can work out most the details, it will be “the end of the game” according to my advisor. He also informed everyone in the lab not to talk about my project to outsiders during its infancy. Last week, a former postdoc in my lab who was fired for multiple unethical conducts blackmailed my advisor to find him a new job, otherwise he would disclose what knows of my project to everyone in the field during his postdoc application. Although it is not sure if he has done so, my advisor decided to publish what we have right now into a small journal as soon as possible.

I understand that the quality of a paper should not be judged by the journal it is published, but unfortunately as a young scientist I do need the “impact factor” to advance my career. Publishing my work right now means giving up all the experimental details for out competitors to follow up quickly, so that my chance to publish the complete story to a high end journal is much rare.

Would any descent scientist “buy” his information and try to repeat somebody else un-published work? Should I convince my advisor to ignore the black-mailer and resume what we are working on?

The blackmailer had returned to Argentina, but is there something we can do to sue him? Or prevent him from sabotage my work?

Look forward to your suggestion.

Nathan writes:

Dear Team TWiV,

Thank you for posting my daughter’s virus drawing and reading my long letter about biotech patents on TWiV #233. TWiV does a great job on many levels one of which is the fact that conventional media can’t devote the time needed to discuss, explore and understand complex scientific issues.

As you probably know on June 13 the Supreme Court unanimously ruled that human genes are not patentable reversing an earlier ruling from the patent savvy judges in the Court of Appeals for the Federal Circuit. The Supreme Court adopted the US Department of Justice position (not joined by the US PTO) that cDNAs were entitled to patent protection. Amongst other things, they glossed over the cognitive dissonance associated with the similarities between cDNAs and mRNAs.

I’m attaching an article from the National Law Journal regarding the decision (http://www.law.com/jsp/ca/PubArticleCA.jsp?id=1370811370072&rss=rss_ca_news&slreturn=20130514161032). It quotes a friend of mine, Michael Tuscan, a JD/PhD at a leading IP firm, Cooley LLP. Mike was a former patent Examiner with the US PTO. I’m copying Mike on this email, both of us would gladly join you on a future TWiV episode if you would like to discuss biotechnology patents.

Best,

Nathan

Chapel Hill, NC

Mikael writes:

Dear TWIVers, After two years of listening to your wonderful podcast, I was wondering why there has not been any discussion of DRACO. I know that the popular media has blown it way out of proportion so I want a factual examination by the TWIV team. If the hype can be believed every virologist will need to find some other line of work. Please fill us in on the real scoop. Thanks, Mikael (pronounced just like Michael!)

Jim writes:

I hear periodic reference to funding issues in TWIV, TWIM and TWIP, so thought your listeners might be interested in this hour-long podcast on the crowdfunding by several engineers from The Engineering Commons web site as well as the show notes.

Regards,

Jim

Smithfield, VA

Marla writes:

Greetings! I am preparing an introductory pharmacology course for an upper division chemistry elective (Juniors and Seniors). I would like to dedicate part of the course to discussing current problems/recent breakthroughs in the field. Can you recommend one or more of your podcasts that would fit the bill? Thanks in advance,

Marla

Marla Hertz, PhD

University of Alabama at Birmingham