Letters archive 2

For more recent letters to TWiV, see this page.

TWiV 200

Luis writes:

Hi TWiVers!

I am writing to you this time because I have just read a short report in “El Pais” (the highest-circulation daily newspaper in our country) referring to the fact that five “exotic” mosquitos are establishing a permanent home in Southern Europe. This is not really new, since global warming seems to be driving tropical species to Northern latitudes. What I found interesting and probably attractive for you and the audience of your podcast is a series of maps which are produced by the European Centre for Disease Prevention and Control (http://ecdc.europa.eu/en/Pages/home.aspx). They show a detailed distribution of different species of mosquitoes (and also ticks) by provinces within Europe, and apparently are periodically updated.

It is particularly interesting the one that shows the actual distribution of the tiger mosquito (Aedes albopictus), a vector for dengue, yellow fever, West Nile, Chikungunya virus, and others. In fact, there have been recent outbreaks of West Nile virus infections in Greece, and Chikungunya virus in Italy, for example.

If you check the map you will see that specifically, the tiger mosquito appears to be recently introduced and probably expanding in Italy, Southern France, NE of Spain, the Balkans and the Russian Black sea coast.

The link is:

http://ecdc.europa.eu/en/activities/diseaseprogrammes/emerging_and_vector_borne_diseases/Pages/VBORNET_maps.aspx

Thank you very much again for your wonderful show. I am not sure if this e-mail will be read before episode 200, but in any case let me congratulate you all for this achievement, and wish a very long live to TWiV!

Best,

Luis

P.S.: Oh! I almost forgot. It is very hot in Madrid, few clouds, and temperature about 100ºF (37ºC approx.).

———————————————————————

Luis Menendez-Arias

Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)

Madrid, Spain

Nacho writes:

Hey TWiV team,

I’m a first-year bioinformatics student doing my PhD in a virology lab. I visited the NEIDL (the BSL4 the Boston University built) a few weeks ago, and really enjoyed it. During the visit, the director of the center explained that the building has remained unused for more than two years after it was built because local community groups sued Boston University for building what they claimed was a “bioweapons lab”. This is just another example of the importance of educating the public about the true purpose of science –pursuing knowledge.

Anyway, save me a seat for the anniversary episode at the NEIDL in September. I discovered your podcast a few months ago and you’ve been a constant motivation for me to explore the virology world. I especially enjoyed the Lassa episode (back in #9) and the incredible story of my compatriot, Jordi Casals, since I’m currently working with Lassa and other hemorrhagic fever viruses.

Best,

Nacho

Robin writes:

The invincible Vincent & crew,

Here is the weather in °C:

http://www.accuweather.com/en/us/fresno-ca/93703/hourly-weather-forecast/39239_pc?unit=c

(at the very top of the page (above the ad banner) on the right side is the switch : °F°C.

In the location box below the ad banner you can type in the city & state or the zip code to get your location. I have it set for my location.

Kenneth Stedman writes:

As a TWiV “bump” I am starting a collaboration with Adam Abate at UCSF based on our TWiV chat.

David writes:

Hi Vincent

Just a quick email to say that I recently found TWiV and enjoy it greatly. I will try to branch out into TWiM and TWiP when I can, as well as making my way through the back issues – I’ve no idea how you’ve got the time to do all of them!

I’ve only recently gotten into the sciences and will be starting a physical therapy degree in September. During a preparatory health science course in basic biology and chemistry which I took over the past year, I’ve found myself much more fascinated by the small-scale physiology and microbiology side of things than the large-scale anatomy, leading me to find TWiV. I am contemplating pursuing some sort of research route after I graduate (e.g. into muscle or bone physiology), although it’s still very early days of course. I was wondering if you or any of the team had ever come across anyone who started out with a larger scale focus in biology and “zoomed in” toward something only distantly related, perhaps even someone from a physical therapy background? Coming into the sciences after having only really studied the humanities feels a bit like being presented with an enormous buffet after having gotten by on oatmeal all my life!

Many thanks to you and the team for putting out a great show every week.

Best wishes

David in the UK

Ayesha writes:

Dear TWIVnauts,

I am responding to your navigation of the Reforming Science in I&I papers on the show. I was a bit disappointed at how you covered them. At times the hour sounded like a list, rather than a discussion. It’s a lot better that than not having talked about it at all, so for that thanks.

Are there training fellowships for women academics who might be coming back after family leave in North America? Wellcome has these in the UK. Maybe this is a way to address one of the leaky pipelines?

Remember that you have a great deal of influence with what you have created with your podcasts. Look at what happened on the flu papers: TWIV had an effect some would argue a huge impact! Look at what you have already achieved with respect to changing some ordinary peoples’ view of scientists! People are listening, people are looking to you guys to help come up with other ways to reform, not to tell us what we already know (that changes will be hard to achieve and unlikely). I don’t think it’s helpful to say that many suggestions from the reforming science papers won’t work: maybe instead like Rich said, let’s come up with new innovative ideas for solutions rather than saying change is unlikely.

Thanks,

Ayesha

Alicia writes:

Hello,

I’ve been faithfully listening to the TWi-fecta for quite some time now and I enjoy them all thoroughly (though I don’t know that I’ll ever be able to catch up on all the old episodes of TWiV). I hope you won’t mind another self-serving, advice-seeking question.

I always listen with great interest to your answers to students as I am just finishing my undergraduate degree in microbiology. However, I’ve noticed that all of the questions directed to you are in regards to continuing on in academia.

It’s taken me a few semesters of laboratory placements, a well timed discussion by your pannel of experts, and a few months of reflection but I’ve decided that I might not have the drive to continue on in academia. I would be just as happy to be a technician of some sort as a post doctorate fellow, which is not at all how my peers feel.

I intend to work in one of my professors’ labs in the spring to determine if I am cut out to be a grad student or not but in the meantime I have much to think about.

I’ve found that in Canada, and abroad, all that is really promoted in universities seems to be research and development as nothing else is ever discussed. I’m beginning to feel like there IS nothing else. While I consider all of those involved in the TrWi-fecta to be at the top rung of the academic ladder I also believe that you’ve had much experience with the wide variety of microbiology based occupations. In your opinion, what can I expect to find outside of academia?

Thank you again for all of your effort on these podcasts. They fill my days 🙂

TWiV 199

Nels writes:

Dear Vincent,

A note of gratitude to you and your crew for generously “interrogating” my recent paper on the experimental evolution of vaccinia virus.

BTW, it was evolutionary biologist Leigh Van Valen (not Richard Dawkins) who proposed and coined the Red Queen Hypothesis in 1973. Leigh was a true character and early advocate of open access publishing. His original manuscript on the Red Queen was published in Evolutionary Theory, a journal he created and self-published at the University of Chicago; still available free and now online at leighvanvalen.com, along with some interesting stories about this unconventional and brilliant scientist who recently passed away.

Count me as a new listener and fan of TWiV!

Best wishes, Nels

Nels Elde | Ph.D.
Assistant Professor
Mario R. Capecchi Endowed Chair of Genetics
Department of Human Genetics
University of Utah Salt Lake City, UT

www.cellvolution.org

Marian writes (re Red Queen’s hypothesis):

from Wikipedia,

“Originally proposed by Leigh Van Valen (1973), the metaphor of an evolutionary arms race has been found appropriate for the descriptions of biological processes with dynamics similar to arms races. Van Valen proposed the Red Queen’s Hypothesis as an explanatory tangent to his proposed “Law of Extinction” (also 1973), which he derived from observation of constant probabilities of extinction within families of organisms across geological time. Put differently, Van Valen found that the ability of a family of organisms to survive does not improve over time, and that the lack of correlation between age and extinction is suggestive of a random process[3]. The Red Queen’s Hypothesis as formulated by Van Valen provides a conceptual underpinning to discussions of evolutionary arms races, even though a direct test of the hypothesis remains elusive, particularly at the macroevolutionary level. This concept remains similar to that of a system obeying a self-organized criticality.[4]”

Tommy writes:

Dear TWiV crew,

I was listening to TWiV 198 and the Red Queen hypothesis of antagonistic coevolution was brought up. I thought I should make a correction regarding the originator of the Red Queen hypothesis. You attributed it to Richard Dawkins, however, the term “Red Queen hypothesis” was actually coined by the evolutionary biologist Leigh Van Valen in 1973*.

*Van Valen, L. 1973. “A new evolutionary law” Evolutionary Theory 1: 1-30. Link to full text here: http://dl.dropbox.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf

You can read more about Van Valen in this obituary here: http://articles.chicagotribune.com/2010-10-24/features/ct-met-obit-van-valen-20101024_1_extinction-journals-modern-biology

Love the show, keep up the good work

–Tommy

P.S. I listened to the end so I know that I shouldn’t be hanging out for a show this week.

Adam writes:

Howdy TWiVites,

Loved the recent episode (TWiV 198) in which you discussed Nels Elde’s paper investigating ‘genomic accordions’ of poxviruses. Elde describes in his paper a mechanism of transient gene family expansion that allows poxviruses to rapidly generate variation in genes whose products interact with host proteins, thereby overcoming host defenses. He goes on to refer to this evolutionary game of cat-and-mouse between viral and host proteins as a classical Red Queen conflict.

In the episode there was some musing about the term ‘Red Queen Hypothesis’ and it was decided that the term was coined by Prof. Richard Dawkins in his book of the same name. ‘The Red Queen’ was indeed the title of a popular science book, of the general flavor that Dawkins writes, however it was authored by Matt Ridley and entitled ‘The Red Queen: Sex and the Evolution of Human Nature’ (an excellent read and available from $7.99 on Amazon).

The Red Queen Hypothesis itself was first proposed by yet another great scientist and communicator Prof Leigh Van Valen (University of Chicago). In his 1973 paper ‘A New Evolutionary Law’ Van Valen used the analogy of Lewis Carrol’s Red Queen – forever running just to say put – to explain a self-perpetuating fluctuation in fitness between two or more evolutionary units (species or genes) arising from mutually incompatible optima.

I have to thank you for making this mistake, as it has led me to actually read Van Valen’s paper in full – which I had not done before, despite having cited it in a number of undergrad essays. There is something really enjoyable about reading old papers where the authors wax philosophical (sic) on their topic, and it is a nice change from the dense, ultra-concise papers that are standard these days. Whether this was because they had less data to cram into figures, fewer authors, or the journals were less pressed for space back then I do not know. Maybe all of the above in this case seeing as this article was the first, in the first edition, of a journal that Van Valen founded.

Probably because I have more pressing uni work I should be doing I spent quite a bit of time reading about Prof Van Valen, who died in 2010. He was a pretty amazing guy who wrote on many subjects, taught and was beloved by his students, contributed several original ideas to his fields, founded journals, and even wrote explicit songs about dinosaurs.

I would like to nominate Leigh Van Valen as a pick of the week – by way of his memorial site at Leighvanvalen.com.

A few choice links: Sex among the Dinosaurs – http://dl.dropbox.com/u/18310184/songs/sex%20among%20the%20dinosaurs.pdf A New Evolutionary Law (Van Valen, 1973)- http://dl.dropbox.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf

Kind Regards, Adam
Melbourne, Australia (18C with a chance of rain)

PS: If nothing else, go check out the Acknowledgements section of Van Valen’s ‘A New Evolutionary Law’ (1973).

Josh writes:

Dear TWiV Doctors,

I have a question about the paper discussed last week on the Emergence of Fatal Avian Influenza in New England Harbor Seals.

What I cannot figure out is if they were looking for an Influenza virus from the start. I mean, I assume if you sample a bunch (5 in this case) of seals, you are going to get a bunch of viruses. Did they report the detection of any other viruses in the seals? I listened to your segment again and read the paper on mBio. The paper says this:

Nucleic acids extracted from lung, trachea, liver, kidney, thoracic lymph node, mesenteric lymph node, spleen, skin lesion, and oral mucosa were tested by PCR for the presence of a wide range of pathogens, including herpesviruses, poxviruses, adenoviruses, polyomaviruses, caliciviruses, paramyxoviruses, astroviruses, enteroviruses, flaviviruses, rhabdoviruses, orbiviruses, and influenza viruses.

They looked for a wide range of pathogens, but I can’t find something that says we found ONLY H3N8 Influenza. Am I reading it wrong? It just seems odd that they found nothing else. However, I’m not a scientist, so maybe I’ve misunderstood.

Thanks,

Josh

Simon Anthony replies:

Hi Vincent,

Thanks for the question! Your listener is quite right, we did find other viruses in those animals. I have a strong interest in the ecology of co-infection, so was very keen to see what other viruses might be present. We also found herpesviruses and adenoviruses in addition to the influenza, though none of these viruses were found in all five animals, and none could be linked to the observed pathology. Interestingly, we found three different adenoviruses. Two of them were known seal adenoviruses, and one was actually an avian adenovirus!! So it would seem that avian influenza was not the only avian viruses that spilled over. In addition we performed deep-sequencing and identified some novel picornaviruses. We’re working those up now, but would love to chat more about them with you at some point.

Hope all is well over the road! S.

Scott writes:

New ‘Heartland’ Virus Discovered in Sick Missouri Farmers

http://news.yahoo.com/heartland-virus-discovered-sick-missouri-farmers-213644509.html

Dear Vince,

I’m a fan of your pod casts and thought you might be interested in the article if you haven’t heard of it yet.

with respect,

Scott

Mark writes:

Could you please discuss the relationship between HPV vaccine and GB, also it would be interesting to know what causes GB and its relationship to Polyradiculoneuritis (coonhound paralysis) and MS. Do these diseases have any viral relationship, thanks. i listen to the show while gardening.

[see http://www.cdc.gov/vaccinesafety/Vaccines/HPV/Index.html
http://www.ncbi.nlm.nih.gov/pubmedhealth/PMH0001704/

Justin writes:

Hey TWIV team!

I have been listening to your podcast for only a few months but listen with rapt attention on my way to work each morning. I was shown the podcast by my professor in my intro Virology class during my last semester of my undergrad in Cell and Molecular Biology. I have recently graduated and decided not to immediately re-enter academia for several reasons. The first being I have no idea what type of degree I am going to pursue (MD PhD or hopefully both). Also and largely I am training as an Elite trampolinist with my sights set on the 2016 Olympics in Rio. Unfortunately that means I plan to put the vast amount of my focus in effort in that venue of my life for the next four years and after I retire would like find a school with a good program without worrying where I will be training. Since, that could put me out of school until 2016 I am terrified I will lose my edge for applying for school when the time comes. I am trying to stay sharp with your podcasts and reading articles that pique my interest, but I don’t think it will be enough. My most recent idea is to take the GRE this year and then apply for a masters program in either the biochemistry department or the biology department which includes cell biology, molecular biology, immunology, and virology research areas at a local university. I flip-flop between the two departments because I’ve heard on your show the importance of chemistry education for virology and that my research adviser previously advised me to not educate myself in solely one discipline. My questions to the TWIV team are whether this is a good plan considering my goals and which department you would most recommend for me? Thank you so much and keep putting out the viral podcasts!

Justin
p.s. make sure you watch trampoline in the Olympics, we can reach heights of almost 30 feet!!! Or get excited and take a peek on youtube by searching Olympic trampoline!

Victor writes:

Greetings, Twividese

In episode 191, the subject of working smart and not long came up. When Rich mentioned multitasking, I couldn’t help but think of the lifehacker article on the subject.
It goes on to explain why multitasking (as most people do it) reduces your over all productivity. It’s a great read, and is changing the way I work.

Here is another article on the same subject:

http://lifehacker.com/5041144/debunking-the-myth-of-multitasking

TWiV 198

Edmilson writes:

Dear Vincent,

Great TWIV 197, it is really nice to learn how science was. Fascinating to see how laborious was to do things that nowadays are only “kitology”.

Keep up the great podcast.

Cheers,

Edmilson

Coyne writes:

After watching Mark’s science pick from TWiV 196 (a Youtube channel dedicated to interesting and entertaining videos shot with a slow motion camera), I felt I had to share a link that I came across the other day.

http://www.youtube.com/watch?v=SoHeWgLvlXI

While standard slow motion cameras record at about 5,000-10,000 frames per second, this technology, which is dubbed femto-photography (developed at MIT), captures light at one trillion frames per second. Because of the incredibly small amount of light that is captured with each frame, the videos they shown computationally reconstructed from “millions and millions” of events with “very clever synchronization”. In one resulting video, we’re able to watch a ~1mm long packet of photons travel and scatter as it hits a surface. A proof-of-concept demonstration also shows that the technology can be used to ‘see around walls’ through light reflection and more clever computation, which could be beneficial in biomedical imaging.

Thank you for the podcast. I’ve been interested in viruses and working in virology labs for several years now and TWiV always gives me something new to think about.

-Coyne

Patrick writes:

Dear TWiV crew,

After many episodes of listening I thought some active participation was in order, especially after meeting Dr. Racaniello over drinks at the Brocach Irish Pub during ASV in Madison. First, thanks to the entire TWiV crew for your service to the scientific and lay communities. I think that an enhanced science presence in the classroom (particularly early on) could really be transformative on many levels: more inquisitive minds, more kids amazed at the complexity of life, more logic-based thinking… The point I’m trying to get to is that TWiV is an awesome vehicle to disseminate science, and having done many hours of outreach in classrooms, it’s very empowering to see how many people can be reached. So many thanks, and also a sincere offer to help out the TWiV cause in any way possible.

And now tidbits from the random thought generator of my mind:

tidbit 1) In a TWiV covering an influenza virus in bats there as some question as to the cycle of transmission and whether the virus could have come from insects. This was considered unlikely because insects do not harbor orthomyxovirus viruses, but in fact, this is not true. There is a family of influenza-like orthomyxoviruses (e.g., Thogoto virus, Dhori virus) that are tick-borne infections of rodents (http://viralzone.expasy.org/all_by_species/79.html). Interestingly, selection in insects has resulted in the glycoprotein of these viruses being more similar to baculoviruses than influenza viruses.

tidbit 2) We had discussed an enhanced multimedia interface for ASV. I think that CROI does this really well (http://retroconference.org/static/webcasts/2012/), and the fact that all the talks are free and online hasn’t stopped people from going to CROI.

tidbit 3) Although I hope this is of general interest to the entire TWiV crew, I thought that Rich in particular would find this interesting, and perhaps might result in a TWiV bump for new faculty Nels Edle (lead author) and Harmit (senior author, and my mentor):

Elde et al. Poxviruses Deploy Genomic Accordions to Adapt Rapidly against Host Antiviral Defenses (https://www.cell.com/abstract/S0092-8674%2812%2900870-7)

I hope this finds you all well, and thanks again for TWiV.

Best,

Patrick (its 26 C and absolutely beautiful in Seattle)

—

Patrick S. Mitchell

Malik Lab

Division of Basic Sciences

Fred Hutchinson Cancer Research Center

HHMI

Molecular and Cellular Biology Graduate Program

University of Washington

Ricardo writes:

http://itunes.apple.com/us/app/evolution-making-sense-life/id529832962?mt=8&ign-mpt=uo%3D2

Kimon writes:

Dear TWiV-tians,

Your delightful podcast has helped to steer my interests towards virology and immunology. I studied Mathematics as an undergraduate, and realized that my calling was in medicine while completing the Teach for America program in New Orleans. I will be starting medical school next month at the University of Pennsylvania, and I’m looking for particular directions of research that might be most appropriate for my quantitative background. I’m particularly interested in HIV/AIDS, but very flexible given that I’m just starting out in the biomedical research world. Any suggestions of papers, books, people, or journals that I could seek out would be incredibly helpful as I try to understand where my skills as a “Math guy” would be most useful.

Thank you for sharing your conversations with the world — your work has had a measurable positive impact on my life!

Rohit writes:

Dear TWIV Doctors,

I was just listening to the Twiv#190 where Dr. Racaniello was talking about making TWIV accessible to more people especially in the developing world where people do not have regular access to internet. I think Radio can be a very effective way of spreading scientific knowledge not only in parts of Asia and Africa but also right here in the United States. Have you explored the possibility of using local radio stations such as NPR in United States for increasing the audience base of Twiv and the other two podcasts. I am not sure how much the radio station administrators will be interested, but it is definitely an idea worth exploring further. May be TWIV/TWIP/TWIM already has a listener who knows more about making it happen.

As always, love the podcasts. Please keep them coming.

Thanks

Rohit

_________________________________

Rohit K Jangra, PhD DVM MVSc

Postdoctoral Fellow, Kartik Chandran Lab

Jim writes:

Wanted to make sure you didn’t miss this news item:

“Vaccine Storage 14 mins – This five part digest starts with Greek IT, but the fourth item concerns the very smart idea of using cell phone tower power systems in developing countries to reliably run refrigerators used to store vaccines. A web site with details is here. To download the audio file go to the link, find the title “Greek IT Upgrade, Bullet-Proof Cars in Mexico, Hajj Facial Recognition Tech, Keeping Vaccines Cold, and Rebuilding Tatooine,” right click “WTPpodcast368.mp3” and select “Save Link As.”

Jim

Smithfield, VA

[here’s a direct link to the podcast from PRI’s The World (#358); the story is at 14 minutes into the podcast- you can use the fast forward button; this eliminates the need for the somewhat more complicated instructions and the Vaccine Storage link at the start that leads to adding an RSS feed and not the audio:

http://player.fm/series/pris-the-world-technology/greek-it-upgrade-bullet-proof-cars-in-mexico-hajj-facial-recognition-tech-keeping-vaccines-cold-and-rebuilding-tatooine

Diane writes:

Hi TWIV-ers!

Thanks as always for an excellent podcast (as well as TWIM and TWIP). I especially loved the “how to read a study” helpful hints segments, as it was really nice to hear that learning to read studies is a skill that takes practice and education. And to know that I will have to struggle with reading studies for a while before I’ll be able to really parse them.

[TWiV #169, or excerpt, “How to read a scientific paper;” right click here to download]

Anyway, I recently read a Young Adult book called “The Way We Fall” by Megan Crewe. It’s a story about an island in Eastern Canada (if I remember correctly) where a viral pandemic hits. The fatality rate is high, and the island gets quarantined. I don’t know how accurate the science is, but I thought it was a fun read. Amazon says this is part one of a trilogy, so I guess there’s more, but at the time I finished it, it felt like an actual ending. Not great literature, but a fun, gripping (and quick) read.

Keep up the great podcasting! I love listening and learning.

Stephen:

http://www.amateurmicrography.net/

An online bulletin board community dedicated to photomacrography, amateur microscopy, and photomicrography.

Oh, it’s 9PM and still 32 degrees C.

TWiV 196

Dallas writes:

I am going through the old podcasts, when I have time. Number forty one covered ISA — a salmonid virus with a billion dollar class damages history. When someone mentioned vaccines development, a comments was made about how can you vaccinate salmon.

Most salmon are already vaccinated for bacterial diseases using automatic machines, where the salmon smolt are lined up, given a shot and released. When you have hundreds of millions of fish to deal with, the machines are fast.

To give you an idea of what has happened to antibiotic consumption over time in Norway salmon farms as vaccines for bacterial pathogens have developed (there is a similar graph showing the increase before vaccines, but I couldn’t find it):

Notes: Use of antibiotics (yellow line) and amount of fish produced (blue columns). The numbers on the left side are the tonnes of fish; the numbers on the right side are the tonnes of antibiotics.

Sources: NMD & Directorate for fisheries, as cited in Ministry of Fisheries (2002).

Virus in the wild fish stock are also a significant issue, but as an old marine biologist once told me: nothing ever dies in the ocean, it is eaten alive before it is actually dead. That makes wild virus hard to study, but the source in aquaculture net pens is from the wild.

Don’t believe all the nonsense being spread by the anti-aquaculture activists and the commercial fishermen who don’t like competition. For example, the red pigments used in the diets are the same chemicals that make wild salmon red and the same as found in “red yeast” or red algae sold in health food stores and found in pepper meal. The color added label was politically added by the Alaska commercial fishermen, who were getting economically killed by the quality control possible with farmed fish (no sitting around on the deck for hours before processing).

Omega 3 fatty acids are a required dietary component in salmon feed and they end up with these fats in their tissue, just like wild salmon. One dinner of farmed salmon — or high fat wild salmon species — equals 10 or so of those fish oil pills and tastes a lot better.

I still haven’t run across an episode on shrimp virus that are resulting in consumers paying an extra billion+ dollars per year in their shrimp cost to cover virus losses.

Love your podcast,

Sam writes:

Dear TWiV,

Thanks so much all these brilliant podcasts, especially episode 184 (Reforming Science). Crowd-funding for science is an interesting grassroots mechanism to obtain support for small projects; you’re probably familiar with Petridish already but I wanted to highlight this project http://www.petridish.org/projects/targeting-mosquito-spit-to-limit-virus-transmission. Only 28d to hit the funding target! Would be great if you could mention it on TWiV.

Best, Sam

ps- no conflicts of interest to declare.

Mark writes:

Hi Vincent et al,

In case you haven’t seen this yet:

http://www.courthousenews.com/2012/06/27/47851.htm

Merck has known for a decade that its mumps vaccine is “far less effective” than it tells the government, and it falsified test results and sold millions of doses of “questionable efficacy,” flooding and monopolizing the market, a primary caregiver claims in a federal antitrust class action.

Alabama-based Chatom Primary Care sued Merck on Monday, the week after the unsealing of a False Claims Act complaint two relators filed in 2010.

Those relators, Stephen Krahling and Joan Wlochowski, were Merck virologists who claim in their unsealed complaint that they “witnessed firsthand the improper testing and data falsification in which Merck engaged to artificially inflate the vaccine’s efficacy findings.”

http://www.courthousenews.com/2012/06/27/MerckUnsealed.pdf

All the best

Richard writes:

Hi Vincent and Co hosts

I just thought you should know, since I guess this is deliberate, that what you are doing is working.

So far you have got me to learn more about science, specifically biology, and virology, than I ever thought I would. To the point of working my way up to Kevin Ahern’s bb450/550 molecular biology course on itunes u. Of course I had to start with basic chemistry, so as to understand things like swartzchild radius etc. From there I went to basic biology, as well as all of your virology lectures. I then took a bit of a break, to grow some bacteria and phage, then to use the phage to create plaques. (I wish I had saved the instructions, as it seems the pages have gone away. Though I am sure I can find them on the Internet somewhere.) Right now I’m round 2/3 of the way through the molecular biology course, as mentioned above.

I am sure that you will have had a similar effect on some small percentage of your listeners. It’s taken several years, more or less since episode 1 of twiv, to get here. However 99 percent of what you say, I now understand, including gell electrophoresis, western blot, 16s subunits etc. Etc. This makes listening to twiv much less infuriating, as now I rarely have to look things up, except for things relating to the papers you discuss.

I guess I should give some details of my background, I studied electrical and electronic engineering. I am an engineer working on water and wastewater treatment. In doing this I’ve done some work in laboratories, testing samples of water. I’ve also spent many an hour staring down a microscope, identifying the various types of bacteria, and protozoa that actually do the ‘work’ of treating sewage. Not to mention trying to identify, and find ways to make life difficult for, foam forming filamentous bacteria. (if you can imagine a 1.5 million gallon aeration tank at sewage works, with such foam. Then a strong wind, blowing bus size chunks of foam about…. Well you get some idea of my feelings towards filamentous bacteria). So I wasn’t unaware of biology, but treated it like a car, I could in effect check the oil, water, and simple stuff, anything heavy duty, I would leave to the laboratory.

I hope you don’t mind me blaming you, as it were. I think this an interesting topic, and I’m enjoying learning about it. I guess that was your intention, to spread interest in a topic you clearly love.

If I get the chance, then I will be taking some sort of biology course, with the view to ending up in virology. Though I’m quite settled in my current career, who knows what opportunities the future might hold.

I guess you can file this particular listener, and under the heading “mission accomplished”

Thanks for taking the time to produce the pod casts that you do. I thought I should pass on my story, so you can see just how good a job you are doing.

Regards

Richard

PS.

Please excuse the brevity of the email, but I typed it on my phone.

PPS.

I think I have removed all the auto correct blunders, but if any got through, I can only hope they are funny 🙂

Renato writes:

Dear Professors Racaniello et al,

Thank you for the TWIV, TWIP and TWIM podcasts – I find them immensely interesting, even though my wife forbids me to listen to them during meals – her loss, really!

I am a computer science graduate student at Universidade de São Paulo, Brazil, and I would like to make a suggestion to you.

Recently you discussed an episode of a podcast named “Futures in Biotech”, which I listen to regularly, along with some other podcasts which are “syndicated” in twit.tv.

They have a very interesting podcast about computer security, called “Security Now”. (Hey, that is my pick of the week – a show about viruses that make you poor: http://twit.tv/show/security-now).

The host of “Security Now” does something which I believe you should also do: he pays to have his podcasts transcribed and then publishes the transcription online. By doing this, the contents of his shows can be indexed by Google and other search engines. If your podcasts also had this, I believe many people would discover you by accident, by simply googling virii-, parasite- and microbial-related keywords.

Again, thank you all!

Cheers,

Renato.

TWiV 195

[we began be re-reading part of Deena’s email from TWiV 193 below]

Ben writes:

Hello TWIV Crew,

I must first apologize it has been a long time since I have listened to the podcast but I promise to get caught up. I am seeking guidance from you as fellow scientists here. On a matter of personal and professional development I was curious as to the most effective and sanity preserving ways you deal with pseudo-science and or the complete lack of acceptance of science and evidence based medicine by some people. A little background I am entering graduate school going for a PhD and when I try to have discussions with my non-science friends or acquaintances I get hear a lot of science bashing and evidence based medicine bashing. I know this has been experienced by you all in the show many times, XMRV and chronic fatigue being an obvious example. On a personal level I have experienced it myself but in a strange way, a sort of reversal of the normal paradigm. I have ADHD (Attention Deficit Hyperactive Dissorder), I know its a controversial issue but I have it, and have been prescribed by my physician for some 15+ years now a medication to help me focus. It’s worked for me wonderfully, I did well in High School, excelled in sports, have had great work success, got my B.S. in Biology, preformed independent research as an Undergraduate with great success and now I am going to be working on my PhD. Yet I have people out there that are telling me, I don’t have a disease I don’t need to be medicated (despite the fact that it works and I am successful), I just need more “fresh air” and to exercise and eat right and get more vitamin D and see posters like “Childhood is not a disease, don’t medicate children” I try to have rational, science and evidence based conversations with these people but I am just a crony of western medicine or am only treating the symptoms not the cause, etc. I worry that a child who is in my situation may not get the help I got.

I just don’t know how to deal with people like that who refuse to accept evidence or only accept anecdote when it works for what they believe (not that anecdote is ever a good argument). I am a man of truth, that’s why I love science. It upsets me when people don’t want to hear evidence or don’t accept the scientific method. I tell them questioning is good but you have to also examine evidence not anecdote. I truly want to educate people and greatly enjoy it but am saddened by people who refuse to learn, and worry that people like that could run our country and in turn try to control my life based on unscientific beliefs. Rarely someone is honest enough to tell me they didn’t know something and that I taught them something and changed their mind (and it felt really good, hence why I want to be in an academic setting). How have you learned to deal with people like that refuse to learn. I don’t want to give up on them but is that necessary? Should I just pick my battles? I know your podcast has been extremely successful in educating people, especially outside the academic setting, do you feel like the battle for knowledge and education is being won? Sometimes I actually become saddened that people are not willing to learn, or accept evidence, but I don’t want to let that ruin my career of seeking truth.

I thank you for reading this I know you are all very busy. I don’t expect this to be read on air (if you do feel free to trim it as you see fit) but do sincerely hope for a response of some kind time permitting via email hopefully maybe a few words from each of you since you all may have different opinions, or strategies that have helped you all to success as scientists.

Thanks

~Ben

P.S. My girlfriend and I both went to see Vincents talk at the University of Washington when he was here a while back. Being a Plant Biologist myself and only part time Virology enthusiast it was a bit out of my area but love to support your cause!

TWiV 193

Angela writes:

Hello Twiv,

Welcome to the great state of Wisconsin! I hope you enjoy your stay. I suggest in your free time that you try some fresh cheese curds from a local creamer and maybe some fried ones too. I’m sure that those from the area can let you know where to get the best curds.

Next, thank you for all the hard work you do. As a senior in high school who is passionately in love with viruses, Twiv never ceases to bring joy and an education regarding the world of viruses. It has also provided entertainment while sewing my prom dress and another dress. Twivers aren’t just lovers of science but also creative!

On a final note, a question. As being a senior, I’ll be applying for college and undergraduate positions at college labs. I was wondering if you fine men have any suggestions for the whole process? Should I inform these scientists that even though I have had no opportunity lab experience I have tried to become familar with the world of virology through Twiv and reading books such as the The Great Influenza?

Thank you, Angela

Deena writes:

Dear Vincent Racaniello and TWIV host-ers with the most-ers,

Vincent: To ring your recollection bells: We met shortly in Dublin during the Society for General Microbiology’s Spring Conference and since it was just before your panel interview of Wendy Barclay, my PhD supervisor, and Ron Fouchier, of ferret transmission fame, we discussed the H5N1 influenza virus controversy. At the time I promised to send you an email to request that you and the TWIV team discuss ways that scientists increase serendipitous encounters with new ideas.

Of course there are many ways to learn about new techniques or cellular pathways that might relate to ones research, including reading papers and attending conferences, but I am interested in the activities in between: The once-a-month kind of activities, where you get to interact with other people on your level who are abnormally excited by the nitty-gritty details of molecular biology/virology/epidemiology or immunology.

What drove me to write today is because I was trawling through the literature trying to find a journal article that would entice enough people to attend our voluntary journal club and hopefully stimulate an interesting discussion. We do alright for a department of about 35 Post Docs and PhD Students, we provide pizza and drinks and usually keep about ten participants entertained for an hour. Our Journal Club is run in the traditional way: There is a presenter, who reads an original research article thoroughly and uses powerpoint slides to present the figures as he or she explains them, we ask questions during the presentation and have a general discussion at the end, but there is a little voice inside me that says “this could be better”. Therefore, I would like to ask you, the TWIV-hosts and your listeners to share your experiences of Journal Clubs or other brainstorming/ discussion/ mixers that you have tried and what you have found that makes the experience that little bit extra-special.

Thanks in advance for your input,

Deena

Final year PhD candidate, looking for a new research home

P.S. Please keep the podcasts coming, I’m totally addicted. I have compared TWIV to other’s, such as Cell and the Naked Scientists, which are good, but your focus, linked with the breadth and depth of knowledge that your hosts bring to the table leads to the best story telling around.

TWiV 192

Colm writes:

Do you plan to do any promotion of an #asv2012 hashtag for the meeting in Madison this year? I remember some limited tweeting from Minneapolis last year (in between melting into the sidewalk) but I think TWiV would be a great way to promote it ahead of time, along with using it when you tweet about the TWiV episode to be recorded there. After the discomfort with livetweeting the morning sessions last year it may not be encouraged, but I think ASV could be moving faster in the social media realm.

As you said on twitter, there was a specially designed app for ASM this year, and I know Society for Neuroscience has one too. ASV as far as I can tell doesn’t even have a twitter account and only the barest of Facebooks. With all of the focus on H5N1 (loved the discussion) this seems like the perfect time to expand ASV’s reach on the Internet.

Maybe I’ll apply to run their social media presence once I finish my PhD. Someday.

Richard Compans writes:

No sampling of lymph nodes was done in the case of the in vitro cell migration experiments using excised ear tissue, from which we observed the emigration of DCs.

For the skin immmunization on the dorsal surface of the mouse, we examined the inguinal lymph nodes at intervals post-immunization. We think that several factors may have contributed to our lack of detection of cells containing labeled viral antigen in these lymph nodes: retention of some of the antigen at the immunization site, problems with insufficient labeling, timing or quantitation, or possibly the processing of antigen. We don’t anticipate that any novel mechanism is involved.

Additional work is underway using improved procedures for labelling of the antigen, which we hope will resolve this question.

Best regards,

Dick

—

Richard W. Compans

Professor of Microbiology and Immunology

Emory University, School of Medicine

Yan writes:

I was listening to TWIV on my drive to work today. Just want to let you know that there is at least one paper (by Chris Upton, David Esteban and coworkers) describing the sequence of a vaccinia virus strain derived from a person who experienced complications from smallpox vaccine. Here is the link:

http://www.biomedcentral.com/content/pdf/1743-422x-3-88.pdf

Love the show.

Yan

Ian writes:

Dear hosts (of podcasts, viruses, and more),

I have just finished listening to the excellent Twiv 183 and I can’t help make a certain observation. In this episode, but also generally, it would seem that the Twiv crew may suffer from a case of bioinformatics-o-phobia. I wouldn’t be too concerned as I expect that this affliction is very common, in fact I have attacks from time to time. Since Twiv is so successful at teaching many of the other aspects and techniques of virology, why not confront bioinformatics head on? It would be a blast to invite a bioinformatician or computer scientist onto Twiv to talk about some exciting virology related computational work, and really delve into the details of bioinformatics methodology. I’ve heard awesome explanations of cutting edge molecular techniques on Twiv, but when difficult bioinformatics gets mentioned in a paper on I’m often left wondering what’s going on “under the hood”.

Anyway, keep up the great work,

-Ian

p.s. I thought this was a cool random example of bioinformatics at the cutting edge of virology…it was the first result that caught my eye after searching for “influenza” and “bioinformatics”

Schanen, B. C., A. S. De Groot, L. Moise, M. Ardito, E. McClaine, W. Martin, V. Wittman, W. L. Warren, and D. R. Drake 3rd. 2011. Coupling sensitive in vitro and in silico techniques to assess cross-reactive CD4(+) T cells against the swine-origin H1N1 influenza virus. Vaccine. 29:3299-3309. doi: 10.1016/j.vaccine.2011.02.019.

Jim writes:

Hi Vince, et al,

Just listened to TWIV 183. As usual it was fabulous. Am also a big fan of TWIP and TWIM.

I do think it would help to get a participant to interpret the bioinformatics which seems to be increasingly present in the more recent articles.

Was delighted to have DDD present again.

73,

Jim

Stephen writes:

I’ve been listening to a lot of TWIV, TWIM and TWIP recently. I’m learning a lot and being reminded of a lot.

You touch on insect biology a number of times. But I wonder if you, or maybe a listener knows, of the Racaniello and friends of entomology.

I’m thinking someone should create something very like TWIV, wide ranging but academic, not restricted to agricultural pest management or the global fight against the “bugs are icky” meme, fun but information dense. Of course, my imaginary podcast does not exclude the topics covered in the TWI family.

There must be tons of research going on in insect biodiversity, ecology, phylogenetics, genetics, genomics, (am I being redundant?) systematics, behavior (eg. mimicry), species descriptions, biomechanics (eg. Berkeley IB department), etc. And, of course, the multi-layered symbioses you folks have mentioned. Interspersed with the history of entomology (Darwin was a beetle collector), and descriptions of the orders and particularly interesting species, I think this could be a wonderful resource, with a nearly endless list of potential topics and papers to discuss.

Regarding audience, I would venture that the participants in bugguide.net represent a fair number: http://en.wikipedia.org/wiki/BugGuide (“BugGuide had over 809 million hits in 2010”).

Stephen writes:

In TWIV 46*, you discussed Israel Acute Paralysis Virus in response to an e-mail. At about 34:40, you both chuckled about the idea of putting a radio tracking collar on honey bees.

I remembered posting about just such an experiment several years ago on my animal communication site.

The photo shows a radar transponder on a honey bee <http://acp.eugraph.com/news/news05/riley.html>. That was a 2005 Nature paper, and technology has advanced since then (a couple of examples below, gleaned from a quick Google search).

* I’m listening to the Virology 101 podcasts in order.

http://www.ncbi.nlm.nih.gov/pubmed/21267650

http://www.plosone.org/article/info:doi/10.1371/journal.pone.0019997

Robin writes:

http://www.phdcomics.com/comics/archive.php?comicid=1436

Stephen writes:

A quick email in response to TWiV 181 in which Kathy used APOD as her pick of the week. Rich asked how he could get this as his desktop wallpaper. I have it on my windows 7 desktop, but not as the wallpaper. As seen in the attached images I have APOD at the bottom of the screen in a panel, and shown progressively larger if one wanted to have it alone. A program called rainmeter (http://rainmeter.net/cms/) can display a number of skins/themes. This particular theme, called omnimo (http://omnimo.info/), is designed to look like windows phone 7/windows 8.

As ever, thank you for keeping me informed and entertained.

Stephen

sent by Lance via Twitter:

http://www.guardian.co.uk/science/2012/jul/15/free-access-british-scientific-research?newsfeed=true

Matt Frieman writes:

A handy temperature chart for TWIV

https://www.facebook.com/photo.php?fbid=10151088393626411&set=a.470264641410.262910.60342206410&type=1

Ricardo writes:

Hello TWIV Tertulia.

On TWIV 174 a Google engenier asked for a test that would help him to figure out the respiratory infections on his house. I just found out a test named xTAG RVPv1 and xTAG RVP FAST that are able to qualitatively identify several respiratory virus. Probably expensive, but it is information.

Congratulations on your growing numbers and keep up the wonderful work.

http://www.luminexcorp.com/Products/Assays/ClinicalDiagnostics/xTAGRVP/

Ricardo Magalhaes, Ph.D.

Associate Professor of Microbiology

********************************************************

Faculty of Health Sciences of Fernando Pessoa University

Portugal

Ricardo writes:

Hello Vincent.

(And Alan and Dickson and Rich.)

First off all, I’m sorry for this email because it is a request.

I have already write You about this but I’m really struggling with it.

I can’t find a source of information (help) to prepare laboratory classes for undergrad virology students. Our lab is a teaching lab and the coolest thing I can do, is to find plaques with bacteriophages and that only take two 90 min classes (in 18).

Can you help me here?

My best regards.

Ricardo Magalhaes, Ph.D.

Associate Professor of Microbiology

********************************************************

Faculty of Health Sciences of Fernando Pessoa University

Portugal

Marissa writes:

Hi!

I love TWiV I learned about it from my Virology professor and always listen to it in my car now and at the gym. I was just wondering if you guys would consider making an iphone app so we can listen to it on the road without having to plan it (kind of like the Science Friday one) and maybe a facebook page too get people interested in science! I am the only science major in my family of political science buffs and I am always wanting to get my Dad into listening to these (he listens to NPR since forever) but now NPR has an iphone app which makes things really easy. Just some thoughts… plus I really love your podcasts on oncolytic viral therapy! I recently learned about RNAi therapy ( in regards to diseases) this summer and thought that was a very interesting subject as well.

Thanks for all the podcasts and you guys are really funny, especially when you guys first got your iphone I cracked up! I just recently got one too hehe! Keep up the great work 🙂

Marissa

Charles writes:

Hi.

Might be nice at some point to have a renewed discussion on the ‘incurable wound’ revisited, with the possibilities of rabies virus therapy?

I believe Drs. Willoughby and Glaser could be great candidates for an interesting chat on same.

Also, with the advent of World Rabies Day on 28 Sept, would be ideal to have a mention of a rabies topic that week before, if possible.

Cheers. CR.

—————————

Houston rabies case poses new questions about age-old illness

http://www.statesman.com/news/texas/houston-rabies-case-poses-new-questions-about-age-2274920.html

Varun writes:

Hello Microbiology Crew,

As always the TWiV /TWiP and TWiM has kept itself on the top of my priority list. An i must say keep it up. And all i can say it has kept getting better and better. I have a couple of questions and a few suggestions.

My first question is that is there any chemical that that attacks the geometry of the virus. I couldn’t find any, but did find that the viral geometry once disrupted will cause interruptions in assembly of at least most of the viral machinery. Please enlighten this area. My second question is could you elaborate about DEAD box proteins. This group of proteins has really been difficult to digest intellectually.

I have a suggestion. Since you interview various scientists on the show which really has given all the audience a great peak into current science, it would be fantastic if you could get Stanley Prusiner and Irwin W. Sherman on the show, and talk about their current research. Also i request you to have occasional virology 101. I feel it has now reached near extinction.

I also have a listener pick of the week, if you would like. If you consider Matt Ridley’s Genome as master piece which was picked previously in the show, then i guess his other book “Agile gene” is a step next to master piece. And thats my pick.

Once again thank you for this highly entertaining education prog

Chris writes:

Hi TWiV team (+audience),

I enjoyed your discussion of polydna viruses and Michael Strand’s work. At one point in the discussion, someone (I can’t remember who, now) asked how such a complicated relationship could have evolved in a non-integrating virus-host relationship. I think this is a very interesting question, and wanted to point out some interesting examples of wasp-virus commensalism, which it turns out seems to be quite common. While the polydna viruses are certainly the extreme example–barely viruses at all anymore, really–there are several examples of other relationships where the virus maintains a lot more independence.

There are probably many more examples of this than I am aware of (this is not what I work on), but the first example that comes to my mind should be of unusual interest to Rich, if he is not already aware of it. A colleague of his at the University of Florida (Pauline Lawrence, Dept. of Entomology) discovered an entomopoxvirus in the venom of the parasitoid wasp Diachasmimorpha longicaudata. Unless I am mistaking, it is required for wasp development–appears to suppress the immune response of the host (fruit fly, Anastrepha suspensa). Unlike the polydna viruses, this is a legit virus–replicates to high titer in the fruit fly and contains all its own genes. It seems that the wasp acquires the virus during development in the fruit fly, presumably by consuming infected hemolymph (insect blood). Adult male wasps are positive for the virus, too; but only at very low titer in all body segments. How the female concentrates the virus into her poison gland remains a mystery. The virus appears to be perfectly self sufficient in the fruit fly–you can passage it in fruit fly larvae, but it seems to lack any ability to transmit from one to the next without the wasp. Super cool–maybe a virus on its way to integration?

Unless I am mistaking, Pauline has discovered additional viruses in the venom of the same wasp–a rhabdovirus and maybe some more. As molecular biology tools become increasingly available to the entomology community, I expect that we will will see a lot of these type of symbiotic relationships in the venoms of hymenoptera (wasps, ants, bees)–would be interesting to see if it is only the solitary parasitoids or if social hymenoptera also maintain them. The presence of this sort of relationship across such unrelated virus types suggests that there is actually a very large ecological niche for viruses in this capacity, so maybe it is not so surprising that we see the polydna virus story emerging the way it is.

Thought you might think this was interesting–my apologies if you are already familiar. As I said, this is not what I work on, so my apologies in advance to important work in the field which I have undoubtedly failed to mention. I believe Pauline is mostly retired now, but I am sure she would be happy to discuss it with you, Rich, if you offered her some Satchel’s.

Thanks for all the work you do–TWiV is undoubtedly the best podcast out there and has made me a much better graduate student (must have used at least 5 things I learned from TWiV in my qualifying exam).

Cheers,

Chris

Luke writes:

Dear TWiV crew,

You guys occasionally talk about the flaws of the publication and grant review process, so I was wondering what your thoughts were on the recent commentary in Nature regarding an investigation done by AMGEN (http://www.nature.com/nature/journal/v483/n7391/full/483531a.html). They tried to reproduce the results of 53 “landmark” papers in cancer research and were only able to do so for six, even after contacting the labs where the studies were done as well as, in some cases, using their reagents or even physically conducting the experiments in the original labs. Although, as you have mentioned, the severity of this problem is different for different fields (cancer research, due to its clinical applications, being perhaps one of the worse ones), my guess would be that it exists to some degree everywhere. Ideally, as with the XMRV story, misleading results are resolved, but the Nature commentary shows that this is not always the case. And while in many cases such a study could cause some dead ends in the lab, other cases exist where misleading results make their way into clinical trials, large sums of money are wasted, and patients receive treatments that do not work.

I was wondering what your thoughts were on this problem in general and if you had any guesses as to how prevalent it is in virology specifically. You’ve remarked on supplemental data. Especially with Science and Nature, which would like to squeeze in as many articles as possible, the supplement has become a way to have very short main bodies of articles with frequent references to supplemental figures that make the papers unreadable. However, having the supplemental information means that you can publish all the data that is generated, which would allow for others to see any existing inconsistencies and more accurately judge how reliable the study is. As Bagley and Ellis remark, this would mean the stories would become less perfect, but most people who work in biological sciences already know that biology is sloppy and rarely as clean cut as we would like it to be. Any thoughts on how the pressure for complete, perfect stories could be lifted given the existing competition for grants?

As always, thanks a lot for all your efforts to make science accessible to people outside your field. The casual conversational style that the these podcasts have make them a pleasure to listen to after a long day of focusing on small technical details in dryly written formal texts.

Best,

Luke

Spencer writes:

Just as a followup, because there were so many groans about Netter’s cadaver… Its common for the intended anonymity for cadavers to not work out. In Dr Netter’s case, I recall that he specifically wanted the anatomy class to know that it was his body. When I did gross anatomy, my cadaver was still wearing his hospital wristband! It’s a very interesting phenomenon, as the first year of medical progresses: Medical students, who spend inordinate amounts of time in the anatomy lab, go from being squeamish to being very non-chalant around dead bodies.

Again thanks and keep it coming. I especially like the revisit of basic parasitology with Dickson. I hope you don’t run out of parasites of minor medical importance anytime soon.

Lark writes:

Hello TWIVians–

I read in the BBC’s April-June “Focus on Africa” magazine an article by freelance journalist Alice Klein an article about health issues in Zambia. Klein notes that medical professionals in Africa are accusing NGOs of bending to financial incentives when they institute new vaccine programs with newly created vaccines. (Rotavirus was the example used in the article.) The African doctors argue that pushing newly-created vaccines creates neglect of vaccination for “basic” diseases such as measles. I had been under the impression that the profit margin for newly created vaccinations was relatively (?) small–ie., not large enough to influence such funding allocations or disrupt existing vaccination programs. Your (financially disinterested) thoughts? Have you also been hearing Developing World anecdotes about short-changing older, well-proven vaccines in favor of flashier, costlier new ones?

Sincerely,

Lark

lay-reader in Goodrich, TX

Jim writes:

NIH recently offered two presentations that your post-doc and younger listeners might appreciate. They are from the NIH. One deals with “Using Linked-In Effectively: Seventh in the “How to” Series” while the other is about “Careers in Science Writing: Sixth in the ‘How To’ Series.” Both sounded pretty useful. The video version of the Linked-In talk includes visual demos of computer screens so the video version of that one is more useful. Alan might like to comment on the science writer talk. Both talks are professionally oriented and detailed enough to be useful to job hunters, job suppliers, and anyone interested in improving communication skills.

Science writer advocates might also appreciate this item I put in my blog:

Professional Listening – Conversations Network seeks people to listen to podcasts and write summaries of them for which it pays $5 each. The link will produce the application processes which consists of producing a short and long summary of a sample podcast, with photo, biography of the speaker, and resources, exactly what is seen for each entry at this typical page. Once accepted you have to produce two reviews under the eye of a mentor who will get your payments for that work, but payment will go to you starting with the third product. You need a Paypal account where payments are made. It can take a month until you get your first payment and they may be bundled, rather than one-at-a-time. You will be paid to learn!

Jim

Smithfield, VA

Luis writes:

Dear TWiVers,

Once again, thank you very much for your excellent podcast and your service to the community of researchers and educators in the biology field (and specifically in virology). It has been a while since my last e-mail. Don’t worry! You haven’t lost a fan. I haven’t missed a podcast since TWiV 113, when I learnt about your show. Your recent podcasts TWiV 173 and 183 discussing about bats harboring influenza and paramyxovirus, respectively, brought back to my attention a paper published last year in PLoS Pathogens, where using deep sequencing techniques, authors reported finding Ebolavirus-like filovirus sequences in bats from caves located in Asturias, Northern Spain. http://www.plospathogens.org/article/info%3Adoi%2F10.1371%2Fjournal.ppat.1002304

As a native of that part of the country I was surprised and interested on the whole story. Of course, there was no evidence of infection or disease, and there were just (only) sequences, but anyway, I found it very interesting and intriguing. I wonder if this kind of search for filovirus has been carried out in other countries outside of Africa (maybe in the U.S.?).

On a related issue, I recently learnt about a huge virus hunting project known as “Global Viral Forecasting Initiative” (http://www.gvfi.org/). Do you have any information about it? Perhaps, it would be nice to have one of their leaders talking about it in your show…

Thank you very much again for your efforts to promote science in general and virology in particular… and long life to TWiV!

Luis

Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)

Madrid, Spain

Jim writes:

Just in case you haven’t seen this. Sort of timely, after your immunology podcast. Perhaps your son, the game player, can evaluate?

Jim

Smithfield, VA

https://members.fas.org/index.php?q=civicrm/mailing/view&reset=1&id=80

Stephen writes:

I thought you might like to look at Michael Specter’s piece in the March 12, 2012 issue of The New Yorker entitled “The Deadliest Virus.” It might seem out of date at this point, but it’s featured on The New Yorker web site’s new Health section. This kind of article could get cited in classrooms, etc. (The article’s behind a paywall, but the issue is in libraries.)

I’m not qualified to do a point-by-point analysis, but I saw a number of errors–or at least questionable statements.

Of course, some of these points could be called picky. I don’t expect a response; I just wanted to bring this to your attention.

Page 1:

No mention that the 1918 flu was an avian flu. The opening discussion could be read as contrasting avian flu with the 1918 flu.

Definition of “pandemic,” point two: “it would have to kill them [humans]” See http://www.virology.ws/2009/05/23/who-will-redefine-pandemic/ for example.

I’m not so clear on point three: “it would have to spread easily.” How important is “easy” spread in defining pandemic?

Description of the annual meeting of the European Scientific Working Group: were the scientists “astonished” at Fouchier’s presentation? Had it been carried out in secret up to that point?

Description of Fouchier’s work as “simply transferring avian influenza from one ferret to another had made it highly contagious.” My understanding from TWIV’s discussion of the now-published paper is that there was a *lot* of genetic work done on the virus, and that the issue was whether the virus could spread from ferret to ferret at all.

Page 2:

“…they had altered the genetic sequence of the virus in a variety of ways. That had no effect.” My understanding from TWIV’s discussion of the now-published paper is that the genetic work was what made the virus transmissible.

“When Fouchier examined the flu cells…” Maybe he meant “the cells infected by the flu virus,” but I think it’s just a mistake.

“There were only five genetic changes in two of the viruses’ eight genes.” 8 RNA segments, 11 genes, correct?

“Fouchier’s achievement was to place all five mutations together in one virus, which meant that nature could do precisely what he had done in the lab.” The first part of the sentence contradicts the first point I made for this page. And is the second part of the sentence true? Can we assume that any lab-built genetic construct could arise naturally? Of course, in this case, the intent of the research was to investigate what genetic changes would be needed for transmission.

“…a dangerous form of life, manipulated and enhanced by man, had become lethal.” Lethal to *ferrets*.

Michael T. Osterholm is characterized as “one of the nation’s leading experts on influenza and bioterrorism,” and is quoted extensively.

Re: the 1970s H1N1, “Most virologists familiar with the outbreak are convinced that it came from a sample that was frozen in a lab and then released accidentally.” I’ve never heard this. It is true?

“The labs in Rotterdam and Wisconsin where the H5N1 ferret work was conducted were both BSL-3 facilities.” My understanding from TWIV’s discussion of the now-published paper is that the work with the actual genetically manipulated H5N1 was in BSL-4. Did I get that wrong?

Page 3

“Fouchier’s virus, which now sits in a vault within his securely guarded underground laboratory in Rotterdam, has fundamentally altered the scope of the biological sciences.” Seems like hyperbole to me.

Osterholm: “Those researchers have all of our lives at the ends of their fingers.”

“worldwide pandemic” is redundant.

“Fouchier hoped to characterize the properties that make the virus so much deadlier than others.” Deadlier to what?

Page 4

“Once you create a virus that could kill millions of people.” Is there evidence that this is true?

Thomas Inglesby”s quote seems to contain some assumptions:

“turn a lethal virus into a lethal and highly contagious virus” Lethal to what? Contagious in what?

“publish how they did it so others can copy it.” Well, other virologists with the proper facilities and expertise and institutional approval could copy the work. Isn’t that the core of scientific publishing? (There’s an important point here. What kind of lab is actually required to replicate this kind of work? What would it cost? How much eduction and training would a staff need? What size staff? Could all the equipment and reagents be acquired secretly? I suspect the mention of “garage” is bogus.)

“As biology has become more accessible, the balance between freedom and protection has become harder to maintain.” What does “biology has become more accessible” mean? Is scientific publication about “freedom”? Does suppression of publication equal “protection”?

While a slippery-slope argument can easily be ridiculed, both of these statements seem to me to be at least partly aimed at biology eduction.

Page 5

“It is not clear when or where the research will continue.” If The New Yorker had delayed publication for a month or two, this would have become clear.

The whole discussion of Rob Carlson’s blog post on home meth labs and e-mail hacking seems irrelevant or barely relevant.

Sizun writes:

Greetings Twiv-ters!

Hi, I’m Sizun Jiang, a graduate from Wisconsin-Madison and waiting to enter grad school in the Harvard Virology Program. I am currently residing in Singapore (where the weather is 29C and 84% humidity, but usually it is 33C and a gazillion humidity).

I have always been a great fan of viruses, and have always been interested in using molecular virology as a tool to understand ourselves better. Interestingly, although I have yet to actually had the chance to work on or with viruses, I have been lucky enough to have had a great education from established virologists like Paul Ahlquist, Ann Palmenburg, Rob Kalejta and Thomas German. Sadly, I never had the chance for any interactions with Yoshi Kawaoka 🙁

Ever since discovering your podcast 2 years back while researching for virology programs for grad school, I AM ADDICTED! It is hands down the best podcast I know! It is a great source of information for anyone on viruses, and always a great way to keep up to date with current information both with-in and with-out the virology world, while learning about scientific writing, ethics, biosafety, etc, with a healthy dose of humor mixed in! I love leeching off all the great information from Vince, Rich, Alan and Dick. Although the latter may be more for anecdotes 😛 Oh I jest.

Twiv is a great companion for me when I go for long runs, giving me a comprehensive workout both physically and mentally. I have always wanted to write in to Twiv, but have yet to come across anything interesting to share, or anything fun to contribute. That changes today!

Here is a great listeners’ pick for you guys:

http://itunes.apple.com/us/app/plague-inc./id525818839?mt=8

It’s a little game called plague inc, which I just came across and was hooked on. Of course my first reaction was: I gotta share it with Twiv! In the game, you play the role of viruses, bacteria, prions, etc as you try to mutate your strain to infect and wipeout the whole world, starting from patient zero! Think of it as epidemiology for pathogens. I highly recommend trying this out on an ipad, although you can play with it on the iphone too!

All in all, keep up the awesome work! I look forward to many more episodes of great fun and great learning from Twiv.

Cheers,

Sizun

Lance writes:

Dear Vincent & team,

I thoroughly enjoyed your podcast on reforming science – very thought provoking. There was, in my view, one thing missing from the discussion (and from the articles) though it’s of a slightly different nature and not such a systemic problem. That is: improving management and leadership in science. This is a problem in common with the only other field I have direct experience of, the field of clinical medicine. In both areas, at least until relatively recently and still persisting in many quarters, exists the dogma that being good at something also means you will be good at managing other people doing that same thing. This is most definitely no so in my experience, and I have seen some truly appalling efforts at trying to manage and motivate a group of people. This is something that most scientists have no formal training in, and nor as far as I can tell does it play much role in promotion or the awarding of funding. You can have the best ideas in the world but if you can’t work effectively with other people they aren’t much use. Paying more attention to the role of management and leadership in science would lead to greater productivity in my view.

Thanks again for a great show,

Lance

Richard writes:

Hello Vince, and co-hosts (I’m never quite sure who will be on the podcast, you swap things about quite often, this is likely a good thing)

The weather here in Weston super Mare, England. It is cloudy and 11 C, though it will get warmer and brighter later in the day.

It’s just a quick note, I’m sure you have already heard of the genome compiler project. I’ve just found out about it from Twit, they have an interview with the creators, it is twit live special 126 (from twit.tv).

I haven’t yet decided if I like the idea, but it seems like the beginning of something big. I guess time will tell. I can see that this is something that the human race needs, but I’m not sure if the potential to do bad things outweighs the benefit.

I must get to work, unfortunately, however I’ll have the latest episode of twiv to listen to, while on the way.

Thanks again for the podcasts, keep up the good work.

Regards

Richard

http://twit.tv/show/twit-live-specials/126 and www.genomecompiler.com

TWiV 191

Russ writes:

Hi Vince and the TWiV crew

I love the podcast. It keeps me in touch with lots of basic research in virology which I would otherwise miss.

I do pediatric infectious diseases and you can imagine how much time we spend dealing with viruses. In my spare time, I do hospital infection control. I wanted to comment on your questions about this statement in the Fouchier paper: “The pandemic and epidemic influenza viruses that have circulated in humans throughout the past century were all transmitted via the airborne route, in contrast to many other respiratory viruses that are exclusively transmitted via contact. “

In hospital infection control, we institute isolation precautions based on the usual route of transmission of the organism of concern. These are in addition to Standard or Universal Precautions which apply to all patients to prevent exposure to blood and body fluids. The guidelines come from the CDC and are for the most part evidence based. They are:

Airborne: These are organisms that can spread by small airborne droplet nuclei for distances of greater than 3-6 feet. The list is pretty short and includes tuberculosis (not a virus!), varicella-zoster virus, measles, smallpox, SARS, and avian influenza. It was also applied to the 2009 H1N1 influenza but probably wasn’t necessary. It is known that VZV can go under the door and infect someone down the hall.

Droplet: these are spread by large droplet particles that spread no more than 3-4 feet after a cough or sneeze. Lots of organisms here but the principal respiratory viruses that fall under this are seasonal influenza, rhinoviruses, and adenovirus. Also includes other infections such as mumps, diphtheria, rubella, pertussis, Mycoplasma pneumonia, Parvovirus B19, plague, group A Streptococcus, and patients with meningitis caused by Haemophilus influenzae type b and Neisseria meningitidis, where respiratory carriage is expected.

Contact: spread by hands and other forms of direct contact (stethoscopes). The main respiratory viruses here are respiratory syncytial virus, human metapneumovirus, and parainfluenza viruses. RSV (not Rous Sarcoma virus) is a huge problem in children and also in the elderly and immunosuppressed. No vaccine yet, and there is a huge need. I have attached a quite old but instructive clinical study showing that RSV is spread by contact and not through the air – at least not as far as 6 feet. The set-up is not dissimilar from the model for showing airborne transmission in the ferrets! In case you are wondering, folks with lice also get contact precautions….

So flu gets droplet precautions and RSV contact precautions. Go figure…

Keep up with the great podcast

Russell Van Dyke M.D.

Section of Infectious Diseases

Department of Pediatrics

Tulane University Health Sciences Center

Natasa writes:

TWiV 190

Cara writes:

Hello Vincent and Team TWIV,

I love Virology, and it is with much chagrin that I admit I have only recently started listening to TWIV. However I have tried to mend the error of my ways by: 1) proselytizing the benefits (keeping up-to-date with and learning new virology) and fun (the weather and witty banter) of listening to TWIV; and 2) now also sucking up to Team TWIV (check).

I enjoyed listening to the recent webcast with the five postdocs in Glasgow. At the end, you had mentioned that you would be interested in chatting with some postdocs at ASV in Madison. I will be attending ASV and would be excited to chat with you.

My adventures with viruses first started with serosurveillance of rotavirus strains circulating in sub-Saharan Africa. After moving to the US, I completed my Ph.D. degree with Dr. Rebecca Dutch at the University of Kentucky studying the unusual proteolytic processing of the Henipavirus fusion proteins. I am presently a postdoc with Dr. Peter Sarnow at Stanford, where my research has focused on the rather interesting interaction of Hepatitis C virus with miR-122 and cellular RNA granules. I am also thrilled to mention that, as of September I will be an Assistant Professor at the RNA Institute at SUNY Albany.

I look forward to the opportunity to meet you at ASV.

Regards from a Postdoc and Assistant Professor in Waiting,

CARA

Jim writes:

This is a 2-column version all on one page for easier scanning, though the print is smaller.I’m Dutch and start slow, but just keep slogging away.

Jim

Smithfield, VA

Sizun writes:

Howdy again Twiv-ters (Twitters, get it?),

Its me again, emailing from Singapore, where the weather is really hot and sunny at 32C.

It is great that the 8 month long H5N1 saga is drawing to a close, with the publication of the Fouchier paper in Science. Indeed, Science can only progress with publications, and I am always a big fan of open access (why should research that is done using public money be restricted from public access?). It is great that the Fouchier paper, along with the many commentaries, are freely available in the online Science magazine website.

I would like to draw your attention to one of the interesting accompanying analysis by Martin Enserink titled “Public at Last, H5N1 Study Offers Insight Into Virus’s Possible Path to Pandemic” (http://www.sciencemag.org/content/336/6088/1494.full). In paragraph 10, Martin clarifies a statement from Ron that called the ferret passage approach “really stupid”. Turns out, the Dutch word of “simple” (which I believe is simpel) is also used for “stupid”. I have only managed to verify this via the mighty google translate, but it would be great to have a native Dutch speaker verify this. However, it is interesting how this one statement was misinterpreted to show that Ron regretted doing the experiment, which I highly doubt he does, after watching the TWIV episode in Dublin. What he is doing is a time-tested way of adapting a pathogen to a new host, and is great basic science.

I would like to thank you and the gang for your great coverage, and clarification of the whole event, right from the start (when I was applying to grad school) till the end (where I will be embarking on grad school). It has been great to hear your analysis and opinions as the events unfold, and the breakdown of the Kawaoka paper when that came out. Now that all these great information is readily available on the internet on your website and in TWIV, I think it will serve as a great textbook example on the fears of new knowledge, and how a lack of information and knowledge on a subject can cause a great amount of unwarranted fear.

I would also like to suggest an interesting paper, also hot out of the oven, in PLoS Computational Biology, titled “Standing Genetic Variation and the Evolution of Drug Resistance in HIV” (http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002527). It is an interesting model that a population geneticist builds, using publically available clinical information on anti-HIV drugs, to suggest that pre-existing mutations in the HIV population may be the root cause of HAART treatment failures. Of course, there any many assumptions that have to be made to keep a model simple (the great old KISS theory), but the main one that was undertaken was that a single mutation was enough to confer resistance. How well would you think this assumption (and subsequently, the whole model) hold up in real life? As we have seen in the H5N1 papers, we need multiple mutations even in the relatively small sialic acid binding site to confer a change in specificity. Also, these single mutations would probably have to be close to or within the active site or drug target site of the target enzyme (say the protease, or RT) to be effectively conveyed resistance via a single amino acid change. Im not sure if the author accounted for this fact (that a single mutation in a specific region of the HIV genome, and not just a random part of the genome, accounts for resistance). If not, would the model still be as effective?

Sorry to bore you with this long email. You can wake Dickson up now (just kidding, I love your TED talk by the way). Once again, thank you all for everything that you have done so far in educating the world about viruses, and keep up the great work! I will continue looking forward to your next episode of TWIV!

Cheers,

Sizun

Naureen writes:

Hello,

My name is Naureen. I am an undergraduate first-year student at Columbia University. I am amazed by the TWiV site. I wanted to ask if there any internship opportunities or volunteer positions available for someone like me.

Thank you very much!

Mark writes:

Dear Dr. Racaniello and co.,

You say in TWiV #175, which spoke about microneedle injections of flu vaccine in mice, that there were no dendritic cells with flu found in the mice lymph nodes used, which begs the question of what happens to the dendritic cells that have been shown to leave from the skin tissue. Since the experiment to see whether these dendritic cells left the skin was performed in vitro, would there be any issue with getting these cells to lymph nodes in vivo from skin tissue? Also, where did they get the lymph nodes that were tested for flu-bound DCs? I would believe that lymph nodes closer to the injection site would be more likely to have the relevant cells, but then again the location shouldn’t make a large difference. Ultimately, I guess what this question comes down to is this: they didn’t find flu dendritic cells in the lymph nodes of these mice, so how do you explain their immunity? Is it likely an experimental aberration or a new mechanism that has gone undiscovered until now?Thanks,

Mark

From a student in my virology class:

Dear Twiv experts:

On a recent episode (174) you had discussed a question raised by a listener about the validity of informative flyers that are distributed to all blood donors. I was happy to see that Twiv was recently featured on the main iTunes page, and consequently garnered many more followers. However, despite the fact that Twiv is free, I was wondering what you would consider to be the most effective way to communicate basic facts about virology to those who might not have access to wireless, or those who might not regularly attempt to further educate themselves (think globally). Are flyers the best bet, or are you forever confident in the powers of the internet? I know that there are several international initiatives to increase awareness about HIV and other major public health issues, but do you foresee a future where education about viruses will be one of these top-tier concerns as well? I?d be interested in hearing your thoughts!

Best,

A recent twiv addict

Lance writes:

Hi Vincent,

I’m a bit behind I’m afraid but I’ve just been listening to TWiV 180 – and you were asking about the sylvatic cycle of dengue.

My understanding of this is in line with what Alan said – yes there is a sylvatic cycle of dengue, and there’s probably a little bit of cross-talk going on in both directions but the overwhelming majority of dengue infection of humans occurs by transmission from other humans not from the Sylvatic cycle, so in current public health terms the sylvatic cycle isn’t that important. It’s importance is more in the potential for emergence of a future serotype of dengue in humans. I have attached a good review on the subject.

I also had a comment on TWiV 172, in which I thought you did a great job explaining a complex paper. You were talking about the potential for experiments in mice without any CD8+ T cells, if I remember correctly. The problem here is that if mice were KO for CD8+ T cells then they could then be sensitive to measles encephalitis. There are models where you can make mice that have transgenic T cell receptors so that all the T cells in the mouse are specific for one virus, or one antigen/epitope. I’m pretty sure these don’t exist for measles (as this doesn’t infect mice normally as you point out) but it might be possible to make them – in other words you have a mouse that has measles-specific CD8+ T cells, but as far as LCMV is concerned it has no CD8+ T cells (because they are all specific for measles). Then you would have measles-specific CD8 T cell immunity but no T cells as far as LCMV is concerned. If that abolished disease you could be fairly sure that LCMV-specific T cells were required for disease to develop. I don’t know if there’s a way to selectively paralyse the T cell response to only one virus.

By the way you met my boss, Tom Solomon, in Dublin recently and I hear he’s going to do a TWiV with you later in the summer – that’s great news!

Keep it up,

Lance

Alex writes:

Dear Vincent!

3 years ago I was writing my master’s thesis on Rhinovirus, so I was a great fan of your show. Now I’m back, infected with HIV (so to say) and you’re still here with your shows and lectures. Amazing! Many thanks!

Alex

Claire writes:

Dear Virology Experts,

My name is Claire, and I am a 3rd year PhD student at Colorado State University. I study a retrovirus called Walleye Dermal Sarcoma Virus (WDSV) in Dr. Sandra Quackenbush and Dr. Joel Rovnak’s lab. I dearly love listening to your program in the lab, and look forward to days where I’m by myself so I can listen to episodes I have missed. I call these TWiV marathon days.

To get to the point, I recently listened to episode 163 “What Rous Wrought” and really thought that you gave a great introduction to the beginning of viral oncology. However, there was one statement that didn’t rub me the right way. One of you mentioned that viral induced tumors are an accident of the viral infection, occurring out of chance due to the virus messing with the cellular machinery. You guys make this statement a fair amount on TWiV (episodes 162 and 174), and this statement is correct for many of the oncogenic viruses out there. However, this is not a completely true statement, and WDSV is one example of an exception.

WDSV causes seasonal dependent tumors in walleye fish. The seasonality of the tumors correlates with the reproductive cycle of the fish, and tumor formation and regression is required for spread of the virus from fish to fish. Let me explain, a naive fish is infected with the virus during spawning when virus is found at high concentrations in the water. The newly infected fish is disease free though the summer, however in the fall tumors (dermal sarcomas) form on the surface of the fish. These tumors grow and proliferate through the winter. During the time of tumor development and proliferation, there is no viral particle production and only two viral proteins are produced (RV-cyclin and the orf b protein). These protein are coded by open reading frames (orf’s), orf a and orf b, that are in addition to the gag,pol and env genes. Things start to get really interesting in the spring, when the expression profile of the virus changes and new viral particles are produced. At this time, the tumors start to regress and eventually fall off the fish. The shedding of the tumors releases the new viral particles into the water, and this is timed to occur at spawning. This is the only time of the year when massive amounts of walleye congregate together, allowing for efficient spread of the virus. At other times of the year, walleye are spread out around the lake in small schools. The life cycle of WDSV is clearly dependent on tumor formation and regression. Without the tumor, as well as the correct timing of tumor development and regression, WDSV would not be transmitted as effectively, if at all. After the whole ordeal, the fish that had the tumors the previous season will be fine for the rest of its life, and will never develop tumors again.

I’m sorry for the lengthy email, but it might be a good idea to get away from the “tumors are an accident” statement. Keep up with the wonderful work, and I hope that you are going to be doing a lunch episode at the ASV meeting in Madison this summer.

Cheers,

Claire

Stephen writes:

Hello twivuminati,

Listening to you guys talk about money spent on science reminded my of this image. I don’t know how accurate it is but it’s an interesting way of displaying the information.

http://www.deathandtaxesposter.com/

Love the podcast and listen every week. I hope it continues for a long time. Thank you for taking the time to do it.

Kristoffer writes:

Hello twimerrinos!

Thank you all for a great family of podcasts that lasts! Here is a link, which I think, can help persons understand papers of the scientific kind, and to feed the knowledge gland!

Here just below the arctic circle, we still have snow, which blow(s). The thermometer says 33f, time to turn up the heater!

Enough with the rhymes, I’m almost committing lingvistical crimes, here’s the link, oh! I need a hot drink!

http://www.bmj.com/about-bmj/resources-readers/publications/how-read-paper

Best regards

Neva writes:

Hi TWIV fellas,

Harnessing our virus friends:

http://newscenter.lbl.gov/news-releases/2012/05/13/electricity-from-viruses/

“Imagine charging your phone as you walk, thanks to a paper-thin generator embedded in the sole of your shoe. This futuristic scenario is now a little closer to reality. Scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) have developed a way to generate power using harmless viruses that convert mechanical energy into electricity…..”

Reminds me of the Star Trek conundrum of whether the proliferating nano creatures constituted a life form.

Fun with science,

Neva

TWiV 188

Judi writes:

To our TWIV leaders!

If you have a mac with Apps, please go to the app store and download cell images…. I think you’ll have a great time going through them.

One other thing – I listened to your show on science reform with interest but I have one request. Please do not EVER apologize for having the passion and the integrity to follow your avocation of science – or writing – or fishing….

So many of our students are lost because they do not see people who have that sort of devotion and caring about their career work and our kids NEED you to be role models. You all do the TWIVs out of love of the subject, you take thoughtful and justified stands on controversial issues, and you are willing to share yourselves ( and somewhat twisted humors) with your audience. In short, you are good people who care about your work and your world.

Please don’t stop – you are allowed to toot your own horns about this. As they say “it ain’t boasting if it’s true!”

Judi the high school teacher

PS thanks for my professional development.

Katharina writes:

I know that TWiV 166 was specific to a (possible) therapeutic agent against HCV, but I was wondering what difficulties are preventing the development of a viable HCV vaccine — do you think that the determination of the transmitted/founder HCV viral sequence is necessary for vaccine development or are there other factors in HCV vaccine development that need to be worked out as well?

Ming Ye writes:

Hello,

In TWiV 177, when talking about the Schmallenberg virus, it was mentioned that the presence of virus in livestock has not affected livestock consumption and that farmers do not need to notify authorities if a deformed animal (possibly as a result of the virus) is born. This strikes me as a risky policy as we do not know if the virus would mutate and be transmitted to humans. Therefore, I was wondering when and how the governments decide on policies to regulate the sale of livestock when an unknown virus is involved?

Katherine writes:

I just had one question in response to Twiv 173 in regards to the influenza discovered in bats in Guatemala: What are the next steps for monitoring the spread and mutations of this virus? Does the CDC really have enough funding and manpower to follow-up and monitor every new virus that is discovered?

Thanks!

cm writes:

I have heard strong statements about the importance of publication, how “science only moves by publication” and how the scientists have to publish everything, and I can’t help but to agree that it’s very true.

My thoughts are with Wendy’s comment on the censorship that it can possibly block other bright minds from accessing the information which can be detrimental to scientific research progress and discovery.

But as I was reading comments on the TwiV video, I strongly received the impression that such opposition to publishing still exist. Besides all the political pressure that may be present, there was a concern about virulent virus information falling into the wrong hands, like terrorists for example. Are they speaking from previous experiences?

As an undergraduate student just touching upon this subject, I don’t think I know about enough history of virology hence made me wonder.

Was there such an instance where such publication and disclosure of information went terribly wrong or misused? Or is this from too much of Hollywood movies?

TWiV 187

Don writes:

thank you all for sharing your knowledge in such a comprehensible manner. Thank you also for your stand against bureaucratic censorship in the H5N1 research, and your win. I have two questions. Is H5N1 a highly specific test for a human genotype/?phenotype, and if those who died of the disease were sequenced would that give a good estimate of the true risk for the rest of us? Question two concerns the genetic code, AGCT &U Are there reasons of physics or chemistry that make this the only way to archive information, or is it just Mr darwin”s best shot to date?. And why uracil is it a chip of an old rosetta stone? Again, thanks so much for your hard work and excellent podcast.

Gerald writes:

Hey TWIV-ites,

I’m a 32 year old, low-waged data-entry clerk without a college education and I’ve been unsure of what to do with my life over the past decade. It’s not until I listened to science podcasts like TWIS and TWIV that I began to reevaluate what I want in life. Your podcasts jump started me into going back to college to get an Associate in Arts for Teaching Secondary (Biology) for High School or Middle School. Your engaging and insightful conversations gave me something worthwhile to strive for where otherwise I was a little lost. I thank all of you for the interesting conversations and for keeping it on a level that the general public can follow (for the most part). I’m particularly happy when Alan joins the group. I have always enjoyed his stark, careful logic when approaching a perspective or problem brought up in the program. Anyways, keep up the good work for us fans and I’ll be listening down in Miami.

William writes:

Good day again TWiV Doctors,

The ethics statement in the Sim et al paper is geared more towards 1) the use of animals to maintain the colony outside of experimental infections, and 2) using the mice in the host seeking assay. The mosquitoes used in this study are a long colonized lab strain, and are typically maintained generation to generation by feeding on an animal, often a mouse, although chickens are also used.

Hope that this provides a little clarification,

William

Graduate Research Assistant

Department of Biology

New Mexico State University

Kevin writes:

Dr. Racaniello and compatriots,

Something that has come up again and again in discussion over things like chronic fatigue syndrome and influenza is *sampling* and the different medical measures considered.

I just saw a paper published by some computer security researchers at Microsoft who discuss some fundamental sampling problems. Their focus is computer crime statistics, but the problems described apply widely to other fields and make an interesting read:

(1) “a representative sample of the population doesn’t give a representative picture of the surveyed quality”

(2) “outliers can cause catastrophic errors”

(3) “for rare phenomenon we are measuring a signal weaker than the noise in which it is embedded”

And it has a great title: “Sex, Lies and Cybercrime Surveys”

[http://research.microsoft.com/pubs/149886/SexLiesandCybercrimeSurveys.pdf]

For what it’s worth, I’d love it if you had an episode with some computer security folks, to chat about statistics, responsible vulnerability disclosure, and possibly also viruses.

Geoffrey writes:

Doctors:

How Many more Pieces of Biological Machinery Are Byproducts of Viral Infections?

To quote the narrator in the old Tootsie Pop commercials, “The world may never know.”, but I would like to suggest that the venom genes in reptiles and platypuses are just such a mechanism. I admit that I know little about the evolution of the venom systems but a gene sequence search might just show some close matches with either viral or bacterial sequences. It would certainly be fun to find out, one way or the other.

Geoffrey

Robin writes:

Dear TWIV team:

Podcast #179 was amazing. The wasp using integrated viral capsidization genes for a vehicle to deliver its own immunomodulatory genes to target caterpillar cells is Nature more imaginative than the best of science fiction. It compels a further rethinking of basic concepts as to what organisms really are. Cladograms of the tree of life overlook the fusion of mitochondrial lineage with an anaerobic lineage to produce eukaryotes. Viruses are para-organisms that alter properties of cells; their integration into cell lineages is a reminder that nucleic acids are the players and we are epi-epi-phenomena after several layers of emergence overlying them. That includes all of biology and all of what we call “civilisation”!

Tom writes:

Dear Dr. Racaniello and colleagues (sorry, couldn’t think of a more clever TWiV appellation that hasn’t already been used),

As always, I’m very grateful for the show. I have a small suggestion that might help spread TWiV to more people. Many sites and online articles use “buttons” to automatically create links that can be shared on social networking sites like facebook or social news sites like reddit. Reddit especially has a large community of science-appreciative lay folks just waiting to get infected by TWiV. These sharing buttons could appear at the header for each week’s episode, along with the retweet button you already use. I would also suggest these for Alan Dove’s blogs. His recent entry on bee colony collapse disorder was great, and it’s the kind of thing that should be spread online to as many readers as possible.

Also, while I’m writing, I have to throw in my thoughts on the Fahrenheit/Celsius issue. I completely agree that we would all be better off using more of the metric system for weight, distance, etc. But, I’m very partial to the Fahrenheit scale for describing the weather. While zero to one hundred in Celsius perfectly describes the the range of temperatures we use in liquid water-based chemistry and biology, zero to one hundred in Fahrenheit neatly caps the extremes of temperature we experience in most weather. Hundred point scales make sense to me. It just depends on what you’re describing.

Anyway, looking forward to your upcoming two hundredth episode benchmark. TWiV is a great show, and it’s really influencing how science can be communicated.

Best regards,

Tom

Nina writes:

Hello,

This question is not entirely to do with viruses, but I really enjoy your podcasts and couldn’t think of anyone else who would have scientific theories.

I have been reading alot lately about two different topics. 1) how diet and stress impact epigenetic regulation and how, for example, a bad diet may impact gene regulation and lead to disease states. 2) The paleo diet (and other plans) that insist grains are bad for your health–mostly stating that since the eating of grain evolved only, say, 10,000 years ago, humans are not well equipped to digest and this can lead to poor disease states. I can’t find any scientific evidence towards these last claims. It doesn’t seem really logical. This would mean that any agricultural progress is not healthy for us? It does seem healthy to cut down sugar intake, especially all of these high carb beverages out there today, and to limit grains…but to cut these things out all together?

What is your scientific opinion on how what you eat impacts health. Can a bad diet lead to a higher susceptibility to a cold or maybe even cancer? What makes up a good diet? There seems to be so many opinions and non-scientific claims out there it’s hard to discern fact from fiction.

Thanks for any thoughts on this!

David writes:

Since the topic of personal genomics has come up a few times lately, I thought this might be a good pick of the week. It is a Nova program on ethical and other questions raised by personal genomics. How ready are people to know their own genetic code? What would you do if you find out you are susceptible to heart disease? Or what would you do if your genes suggest you are not?

http://www.pbs.org/wgbh/nova/body/cracking-your-genetic-code.html

Cheers

David

Josh writes:

Dear TWiV Doctors,

Here is my selection for a Listener Pick of the Week.

It’s a 2009 editorial in Bioterror and Biosecurity, entitled the “Nuclearization of Biology is a Threat to Health and Security” by David R. Franz, Susan A. Ehrlich, Arturo Casadevall, Michael J. Imperiale, and Paul S. Keim.

Since Dr. Imperiale was on the show discussing these issues a few weeks ago, I thought it would be relevant.

http://deepblue.lib.umich.edu/bitstream/2027.42/78142/1/bsp.2009.0047.pdf

Sincerely,

Josh

TWiV 186

Kurt writes:

Dear Vincent,

Sorry I missed your visit to NU- my teaching duties in Evanston prevented it!

Several of my students attended both and had good reports all around. Your work on ISGs sounds like it is coming along well.

I just today listened to the TWiV netcast myself and not only did I understand the Monty Python references, but I wanted to give the answer to one mystery.

I was the ‘former student’ who framed the Maxam-Gilbert combs for Bob Lamb– In fact there are two- one made by Bob and the other made by me (I needed more wells as I recall). Little did I know that I passed the sniff test back then! Those ~50bp were hard won and very costly compared with the ease of deep sequencing today.

Best and hope to see you next time,

Curt

Jamison writes:

Wow! This episode is bookmarked for relistening. I was really drawn into the scope and frank discussion of core concepts that literally run the world of science as I have come to know it. I have always admired Vincent and companies opinion regarding the need for openness and transparency of science, but even then I had no idea how incredibly dire the need was until it was ranked it terms that your average joe could digest. I assumed that the 21st century system for funding, disseminating, and application of scientific research is primarily based on universally grounded principles itself and it appears that it is just not so. Competition is an essential tool for some areas of science, how much did we gain as an aside because Edison and Teslas ideas fought for supremacy? Never the less it can also cost us unmeasured leaps in human progress when we waste effort competing for the same end. Brilliant astronauts and cosmonauts died fruitlessly because governments define the benefits of competition as gospel rather then dynamic. Discouraging cooperation/collaboration of data amongst scientific experts is irrational far beyond sharing the vapid benefits of prestige and wealth a hundred times over. In words that make the most sense to a tax payer like me: why the hell isn’t the science of science based on the science of science? There is no shades of grey here… A scientist should believe that data and research is either open source or close minded, period.

Ferric Fang writes:

Arturo and I are thrilled and honored that you featured our essays on reforming science in TWiV. I listened to the entire netcast this evening and thoroughly enjoyed your thoughtful and entertaining discussion with Rich and Alan (Arturo is presently traveling and heard it earlier today from Madrid). We certainly understand the general pessimism about achieving a wholesale reform of science. Nevertheless we are encouraged by the interest expressed by scientific leaders such as yourselves and hope that momentum can build for substantive changes that will make science better.

By the way, my parents named me “Ferric” because they had decided to give all of their kids names starting with the letter “F” and wanted a strong name for their #1 son (iron). I’m just grateful they chose the more stable oxidation state.

Thanks so much–

Ferric

Arturo Casadevall writes:

Hello from Madrid where I had the pleasure of listening to the webcast. I thought the discussion was superb. Although I agree with you that change would be incredibly difficult, I believe it is possible because the young people in science are so dissatisfied with the system. Everywhere I go ‘reform’ is the major topic that people want to talk about. We are working on a set of specific ideas. For example, imagine if the Nobel prizes were given for a human accomplishment instead of to a person – what would this do the economics of science? Imagine if the past year the Nobel Foundation had given a prize ‘For the discovery of Toll Like receptors’ instead of singling out two people and leaving a lot out. What if collaborative papers were given higher value in promotion process that papers that come from a single lab? Simple changes could have tremendous impact. I am not naïve enough to think that this would be easy but to me the fact that you and your guests talked about this is already progress for discussion is always the beginning.

Again, thank you for bringing attention and new perspective to the problem.

Arturo

Matt Frieman writes:

Hello Podcast Pioneers, Virology guild members,

I listened to the TWIV 184 on Reforming Science last week and heard the callout to hear my experiences with the life of a young scientist. If you talk to anyone that knows me in science, they will tell you that I love love love this gig. I think it is amazing to have a job where you are doing things on a daily basis that no one has ever done before and when you get a piece of data, it is an answer that no one else in the world has. It is a truly remarkable enterprise that we work in. And I get to share this love of Science with students, techs and postdocs every day.

It is also true this is a rough game sometimes. As a PI, you are constantly being rejected by reviewers of grants and papers who deem your stories insufficient for one reason or another. I am in a constant standoff between spending time writing papers or grants and doing Science. Now with my own lab, unfortunately it is mostly the students and techs doing the work and I get to spend more time at the desk, which I do not enjoy. However it is part of the game we all play.

The other part of the gig that you talk about are the issues with publishing and funding. There is great competition for an ever-shrinking piece of the funding pie. We have been blessed with an RO1 for my research, which allows us to breathe a bit and take the time to do the work the right way instead of rushing to get data for grants. It also allows us develop complete stories for papers rather than rushing out small crappy papers just to build up a CV list for grant review. As discussed in the articles, there is a huge explosion in the numbers of journals, meaning that more crap science can be published in journals that no one reads, again to just make your CV heavier. As for grant reviews, they are getting pickier and pickier. You didn’t talk about the numbers in the show but there are basically only 2-3 grants per study section that get funded from smaller labs. The other 4-5 grants go to the big labs that already have multiple grants and contracts. I have also heard from people on study section that as a new investigator, the chance that I will get a second RO1 shortly after receiving my first RO1 is slim to none. I still try, because I like to prove people wrong, but I know the next RO1 has to have a fully developed story backed by 2-3 papers before it is going to get a funded score.

Another big problem, which is touched on in the papers, is that the next generation of scientists, those in graduate school now, do not want to go into academic science. In my experience, most aren’t even considering academic postdocs. They see the other professors scraping for cash from NIH or other assorted agencies. They think that they will have no chance of getting grants for their own lab since all of the big cheese labs are also scrambling and fighting for the same cash. It is those, like myself, who are stubborn enough to be keep getting back up when you are told NO over and over again. The good news is that everyone is being told NO all the time in this game. However, the future of science will have to change soon to accommodate the changing times.

I don’t know what the answer is. I do think that there should be a cap on the amount of NIH money a lab can get. I do think that there should be more money for training grants for students and postdocs, which will alleviate stress on labs. I do think that we need to talk to the public more about what Science does for them. It is time to get past the next great cancer cure BS that shows up on the Today Show every week. That is not helping our cause with the public. Educating people to how Science really works is the key. Carl Zimmer and Ed Yong do this very well every day. Students out there in high school and college need to be shown how awesome it is to work in a lab. I still have a picture of my first DNA gel I ever ran. Kids are all techies now. We don’t have to dumb it down very much to get them interested. It is time to initiate a new wave of creative and intelligent kids into the guild that we practice on a daily basis. And hopefully, by the time they get into grad school, we will have this whole funding/publishing/grant review mess figured out.

OK, time to finish my plaque assay!

Thanks

Matt Frieman

The University of Maryland School of Medicine

The Department of Microbiology and Immunology

Thomas writes:

Hello Vincent, Alan, Dickson and Auxiliaries 😉

I have come across this apparently new Bunyavirus that emerged in Germany Recently.

here is a link http://ecdc.europa.eu/en/publications/Publications/Forms/ECDC_DispForm.aspx?ID=795

Seems like a pretty strange virus. Hope you guys could do a twiv on it (because it “might” make humans sick too)

greetings from china

Jeff writes:

Hey TWIV,

This is an article I came across and thought of you guys!

http://blogs.scientificamerican.com/observations/2012/02/20/hepatitis-c-now-killing-more-americans-than-hiv/

Your podcast is great! I’ve listened to about half of the TWIV ones in the past month or so.

Thanks for your service

Jeff

Neva writes:

Hi Fellas- Vince, Dickson, Alan & Rich,

Once again I must say I love your podcasts! Thank you for sharing them.

Below is the url for a blog post from my dear friend Ken Wilson of Dripping Springs Texas. He is a person of many talents and interests including expert silversmithing, collections of antique photographs, documents and postcards, kayaking and Texas history.

This blog entry describes finding a shard of pottery that leads to the tale of an incredibly successful (financially) malaria-and-what-ails-you ‘cure: Wm RADAM’S MICROBE KILLER, a patent “snake oil” medicine created in the 1880s by William Radam, a Texas nurseryman who had previously invented several potions to kill blight and fungi on plants.

Sadly, as you mentioned in a recent TWIP, snake oil products -especially for malaria in Africa- is still a thriving business.

http://kgwbreadcrumbs.blogspot.com/2012/01/killer-find.html

Hope you find this interesting,

Neva

Buda, Texas

Simon writes:

Hi TWiV!

Firstly, brilliant show it is very informative and easy to listen to!

I have only just downloaded and started listening the podcast, so am catching up, if this topic has already being discussed please let me know.

I would like to make a suggestion for a show topic…

Viruses, infectious diseases and hygiene

What I’d like to hear about is your experiences with viruses in terms of what protection is needed in the lab. Have you any experience in the higher bio safety levels; what viruses are kept in the various safety levels and why? What happens if someone is accidentally infected by an agent in a lab, are they isolated there and then?

I think it is interesting from a public health perspective to know the process of virus handling safety and how these procedures can be used to influence public behaviour during pandemics.

During the 2009 Swine Flu Pandemic we were advised (in the U.K) to use alcohol gel frequently and cough into the elbow rather than hand etc…This was intended to impair the spread of the influenza. Are governmental guidelines sound or should an individual do more during a pandemic (i.e. stay home) avoid crowded places etc. What measures did you take during the 2009 pandemic?

What hygiene measures would you recommend/ have used for infectious diseases…particularly in public transport?

On another note when someone is tested for antibodies how exactly does the procedure work? Does the researcher look for a specific antibody or is there a testing method that lists/displays the antibodies found in a sample?

Regards,

Simon

Geologist

Ricardo writes:

Hello TWIV members.

Thank you for TWIV 171. All of it, but specially the last part. We truly learn a lot of Virology from this show, but from a long time now I have noticed some other things we can learn (especially students as they are so many, I bet); enthusiasm for what you do, even if it is Science, an enormous desire for knowledge and the ways of getting it in a proper fashion…

This afternoon we learned that it is possible you can make a mistake, it is ok to be told about it, and mainly, it is ok to face it and accept the criticism. I’m proud to recommend TWIV.

Please keep the good work, because You guys are doing it fine.

Ricardo Magalhaes, Ph.D.

Associate Professor of Microbiology

********************************************************

Faculty of Health Sciences of Fernando Pessoa University

Rua Carlos da Maia, 296

P-4200-150 Porto

Portugal

Sven writes:

Dear TWIV team,

I really enjoy your Podcast (Podcasts I should say, including TWIM). I have been thinking about going back to academia for a while now after I worked for ~5 years in biotech. Your podcast helped my decision making significantly since I realized that I want to do more hands-on research.

I am a trained molecular virologist with >10 peer-reviewed papers (http://www.ncbi.nlm.nih.gov/pubmed?term=enterlein) and several years of BSL-4 experience. I published the first successful rescue of a recombinant Marburgvirus from cDNA a few years ago. My dream is to get an academic position at University of Hawaii since my interest has always been emerging infectious diseases and I am sure that my experience could help the Pacific Center for Emerging Infectious Diseases Research, especially with the new BSL-3.

I have been out of academia for 5 years but I hope that this is not too long to step back into academia. Do you have any suggestions for me that could help me in my endeavors?

Many thanks and best wishes from Maryland.

John writes:

I enjoy your podcasts and always learn a lot. The problem is though is that I rarely have enough time to listen to the typical hour and twenty to hour and forty minute program. I respectfully request that you work to reduce program length to one hour. Maybe you could consider shortening the introductory and ending discussions and have less chit-chat in the middle.

John

Jim writes:

I see discussions about the Science-Technology-Engineering-Mathematics initiative, but no mention of bio sciences. Is there a similar initiative under way? Bio science developments are certainly appearing at every turn, so a need for more help must exist.

Thanks.

Sergio writes:

Dear TWI(V)(M)(P)ers:

It has been a long while since I decided I wanted to write to you again, so I ask for your apologies if the ideas on this mail fall all over the place.

When I discovered TWIV I was still a naïve an innocent master student in Japan. I was hooked immediately (kudos to Vince’s son and the gaming chapter). Many years later (also a new iPod, one daughter, a baby soon to come, an earthquake, a tsunami, and a nuclear accident later) I came back to my country (Bolivia) a year ago, with a Ph.D., a family to look for, and many dreams (needless to say, very little money).

Unfortunately, I am still looking for a stable job (Ph.D.’s are not in a high demand in developing countries) but I try to keep up with TWIV, TWIM and TWIP (Sorry to say that being used to a super-fast connection in Japan, it now seems it takes ages to download each episode…but I keep waiting every one of them, although now I am sort of behind in all three podcasts).

Well I am an Agronomist (I bet now Vince knows what that means after being in Brazil) and I specialized in plant pathogens in general (therefore I find all of your podcasts fascinating). My doctoral dissertation was about a bacterial plant pathogen, Ralstonia solanacearum, and its survival in water and soil, so I guess you could say that I am sort of a plant epidemiology/microbial ecology guy. Nevertheless, virology still is fascinating to me (plant viruses obviously) and I learned a lot about parasites as well (nematodes are very important plant pathogens. By the way, where is Dickson lately?). That also explains why I am a little biased in preferring stories about bacteria and fungi.

I have written to you previously wanting to know about dengue fever (I hope I am not suffering that right now: fever, malaise, runny nose, etc. “Welcome to the tropics”), about gene silencing in plants and funding (I am the guy who put Rich Condit in the spot asking for suggestions on how to get funded, sorry about that).

Since I do not have (yet, I am always optimistic) a fixed job, I have been doing consulting jobs (awkwardly enough, for university projects) in biological control and plant pathology. The last of those little jobs brought me to the middle of the Bolivian sub tropic, where I am 8 hours away from the city (my hometown LaPaz) through the most dangerous road of the world (I am not making this up, check this,

http://youtu.be/6by8bxt-rBI

they call it the death road), and I get to teach to tropical agronomy students about plant disease integrated management. It has been one of the most rewarding experiences in my life, because thanks to internet and open access (in which of course the TWI(V)(M)(P) media empire is included) I am able to give to farmer kids, who have never had access to the latest knowledge sources, the best information I can. Of course they have deficiencies (the education system is very bad as you can imagine), but I can see there is potential if these students get the opportunity to get a better education).

So, after such a long intro I have the “weekly pick” suggestion. Since I am a plant pathologist, I have been using for the classes I mentioned, mainly info I found in the American Phytopathological Society website (APSnet). They have education material, suggestions for professors, photographs, lessons, etc. and it is all free! They even hove some material translated to Spanish, Chinese and Portuguese. So I think it is a nice pick for TWIM (since plant pathogens are microbes), and they deserve some publicity for the valuable material they put out there for third world countries. I must say that you are also on the same page, perhaps the language is a barrier, but being completely open you allow bilingual people such as myself to get informed and then pass this information to less fortunate folks. Believe it or not, it is a great service that you can’t always realize from a lab bench in a prestigious university. So there you go, a pick and a compliment.

Another excellent podcast that is on the same vein is “El mundo de los microbios”, which is the podcast in Spanish of ASM (conducted by another Bolivian, go figure!!). There they touch human microbiology but have also dealt with plant pathogens some times.

Finally, as I always do, I would like to suggest some more episodes on plant viruses (in TWIV), and plant parasitic nematodes (in TWIP). I hope this long mail didn’t exceed your patience due to its length. Once again, thanks for your great podcasts, and keep them coming. We will keep listening.

Sergio

Ph.D. in Biocontrol Science

Tokyo University of Agriculture and Technology

United Graduate School of Agricultural Science

Biocontrol Science Department

Instituto de Investigaciones Fármaco-Bioquímicas

La Paz, Bolivia

Gopal writes:

Hello,

I wonder if any one has drawn your attention to this article published in the British newspaper, the Guardian:

http://www.guardian.co.uk/world/2012/mar/28/bird-flu-mutant-strains

The remarks of Dr. Jeremy Farrar, a specialist who has been seeing serious cases of avian H5N1 infections for many years now in Vietnam, are, I thought, particularly noteworthy:

The genetic mutations that made Fouchier and Kawaoka’s viruses so transmissible in ferrets would not necessarily be the same ones that help bird flu jump into humans. But if the details were published, Farrar said he could at least screen for them and learn whether the mutations appear only singularly in the wild, or start appearing in clusters of twos, threes and fours. More importantly, knowing how the mutations transform the virus would help scientists spot other mutations that could make bird flu adapt to humans. “All of this surveillance is not much value if the experimental work, which is mostly done in western labs, is not made available to the countries where it’s most needed. We can’t be blinkered into thinking these are the only mutations that matter, but the information could be important for us,” Farrar said.

People of dying of H5N1 infections in Asia and places like Egypt, not in Europe or America. If the H5N1 virus was killing people in America, would this crazy debate created by the NSABB ever have taken place? I doubt it.

Gopal Raj

Science Correspondent, The Hindu newspaper, India

Stephanie writes:

Dear TWIV crew,

I noticed an editorial in the March 29th 2012 edition of nature asserting that the low success rate of clinical trials based on pre-clinical data was due to the sloppiness of scientists. Isn’t it a bit strange for someone to assume that effective treatments in animal models should necessarily work in humans? Shouldn’t the severe limitations imposed on clinical trials by both cost and patient number be considered here? What do you guys think of this accusation?

[Here’s the editorial: http://www.nature.com/nature/journal/v483/n7391/full/483509a.html and comment: http://www.nature.com/nature/journal/v483/n7391/full/483531a.html]

Howard writes:

Hi TWiV(s),

First, congratulations to Dr. Racaniello on receiving the Peter Wildy Award. Certainly a well deserved honor.

Next, two letters on TWiV #176 strongly resonated with parts of my experience. The letter from the graduate student who was upset at the lack of professional respect shown when a presumed colleague appropriated her intellectual property reminded me of a similar incident when I was a graduate student in Medical Microbiology. In my case the trusted individual Xeroxed my master’s thesis and subsequently got a position at a prestigious research lab working on the same microorganism at Harvard University. He repeated and confirmed my unpublished work and published it without attribution. The upside is that the results helped initiate a couple of research projects by the PIs in his lab and their scientific ability and intellectual prowess resulted in discoveries in areas I might not have investigated. It is satisfying to be part of the process, even if unacknowledged.

The next letter about the possible Epstein Barr Virus etiology of Chronic Fatigue Syndrome also hit close to home. Some years ago my wife and one son were exposed to a diagnosed severe case of Infectious Mononucleosis. They both developed typical symptoms with my wife’s being a bit more severe although her physician was skeptical that she also had Mono because she was almost 40 YO and would be presumed to have contracted it as a young adult like our son had. I requested a more complete lab workup and discovered she had a high titer of anti-EBV antibodies of the IgM class indicating a recent first infection. Her symptoms then progressed over the next several weeks into what we later discovered were “typical” CFS symptoms. Working with her physician, we ruled out other possible diagnoses and an immunological workup at the Cleveland Clinic showed a CD+8 T cell response that was typical for chronic EBV infections and which is associated with CFS. She gradually improved but over the years she has had flare ups with inflamed lymph nodes and nodules under skin and near muscles, generalized pains, and extreme fatigue but symptomatic treatment allows her to bounce back. My suspicion is that having a severe EBV infection as an adult rather than as a youngster or young adult may lead in some cases to the chronic condition diagnosed as fibromyalgia or chronic fatigue syndrome. Maybe this is analogous to having an initial infection with polio virus or the mumps or measles virus as an adult where the infection and sequalae are more severe. However none of the above precludes the involvement of another infectious agent being required for the observed outcome.

And finally, thank you and your crew for the educational and entertaining TWiV, TWiM, and TWiP series. They are good for my brain and the rest of my body too because I often listen to them while working out and have extended my time doing aerobic exercise so as not to finish before the end of the podcast.

Best regards,

Howard, Ph.D.

Mentor, Ohio

Peter writes:

Dear TWiV team.

This research looks interesting, a variation in a single gene (IFITM3) can make influenza life-threating for some people and a relatively mild disease in others.

Particularly interesting to me as I have always been prone to respiratory infections, and they seem to persist for longer than in most people.

http://www.sanger.ac.uk/about/press/2012/120325.html

The protective mechanism is not yet known but if a test is produced to show who has the less effective form of the gene then they could be given preferential vaccinations.

Neva writes:

Hi TWIVers all,

I am sure you have read the interesting Wired Science article “Should Science Pull the Trigger on Antiviral Drugs…”.By Carl Zimmer. Dr. Racaniello is quoted in the piece. It might be a good pick for your listeners.

http://www.wired.com/wiredscience/2012/03/ff_antivirals/all/1

A note on the pronunciation of Buda (Texas). The name origin story locally is that the town was named after a boarding house/eating establishment on the railroad stop run by two widows. The Spanish word for widow is “viuda” so the name became Buda pronounced “Beu dah”. Most folks hereabouts are pretty laid back so if you say Buddah, what the heck.

Love your podcasts,

Neva

Buda TX

Manoj writes:

Dear Prof. Racaniello and the dear old gang,

I’m a big TWIV fan and have listened a lot over the past few years, first walking to and from work at Imperial College London (Dept. Infectious Disease Epidemiology) where it (and TWIP) have really helped me to learn about virology, parasites and biology. My background is in physics and math and I have had to retrain as a biologist (albeit a mathematical biologist). Your chat with Alan, Dickson, Richard and now Michael is terrific fun and very informative! My latest position is in Atlanta, where I have moved with my wife, at CDC. I have been trying to put together projects and people for an infectious disease mathematical modeling unit and, so far, I’m working my proverbial butt off on several projects concerning viral and bacterial infections. But it’s enormously exciting and challenging.

Regarding episode 173 (Michael Walsh’s last appearance): Michael was talking about issues relating to the kind of work I have been trying to kick start at CDC and I would enormously welcome such a chat (please let Michael know and take him up on it)!

Keep up the great work. Your listenership seems rightly devoted and delights in every show.

Yours, Manoj PhD

Imperial College London & CDC, Atlanta, USA

Robin writes:

When an entity is not metabolically active, it is not, at that time, alive. It is living in the context of appropriate time and ecological frames. A mammoth-specific virus recovered from permafrost would be neither alive nor (in this age) living. it could be “reVIVED” if a mammoth was successfully cloned. A virus particle is not alive. In itself, it is not living any more than a human being would be living outside the ecosystem that sustains the human: a human without a spacesuit on the moon would not be alive or living.

Abstracted as an individual entity, a virus particle is no more live than a frozen bacterium.

“Living” can be a verb, unlike •alive”.

Allison writes:

Vincent,

I won’t lie, I’ve taken a long hiatus from listening to your podcast. I blame it on a bad experience with a few virologists and consequently you and my passion for virology were casualties. At the time I was taking a virology class and I found a few of the organizing faculty were rather snotty toward my non-virology background/research. The experience ended badly and I took it as a clear indication that my path was set away from virology. So now a couple years later I have defended my Ph.D. (yay!) and in my pursuit of a post doc in an area of research I am interested in I am once again thinking about virology. But the question remains as to whether a switch is even feasible. Do you have an advice for obtaining a post doc in virology if you are coming from a non-virology field?

Thanks,

Allison

David writes:

Dear TWiV

In TWiV 168, Vincent’s pick of the week was a blog post about the use of technology in the classroom. I’ve tried all kinds of technology in teaching and allow my students to use laptops and ipads in class. The most frequent comment I get however is that the use of one specific technology is most helpful: the oldest technology available in every classroom, the blackboard. Perhaps they assume that if I’m writing it on the blackboard, it must be important and noteworthy.

Also in TWiV 168, a listener’s e-mail asked about endogenous retroviruses and whether they could be removed. Welkin mentioned that those sequences now play an important role in the overall architecture of the genome. I’d like to add to that discussion by mentioning that some of those ancient retroviral integrations are essential in other ways too. Formation of the placenta depends on expression of proteins called syncytins, which drive the fusion of cells to forms the syncitiotrophoblast. Syncytins appear to be env genes of retroviral origin, which of course, have fusogenic activity. A process critical to the development and evolution of placental mammals, thanks to an ancient virus. I wouldn’t be surprised to find other important processes that are the result of ancient viral integrations.

http://www.pnas.org/content/108/46/E1164.short

Cheers

David

Tom writes:

Dear Vincent, Dick, Rich, Alan and whoever your guest is today,

I wrote to you some weeks ago regarding the “So …” preface to answers, and mentioned that my wife’s name for whatever variant of CFS she has as WBD (Wierd Butt Disease).

In addition to TWIV, I’m now following along on Vincent”s W:3310: Virology course in iTunes U. This is a wonderful resource, and is greatly enriching my understanding of the TWIV conversations.

In Lecture 3, a student asks you if there are viruses that tap into the mitochondiral DNA replication machinery. You respond that you (we?) don’t know of any, but there could be.

My first thought was, there MUST be. Mitochondria are often described as symbionts that presumably evolved from some independent life form. Over the course of evolution it’s hard to imagine that distant ancestor staying immune to viruses. If nature provides a resource (such DNA replication), some other aspect of nature will evolve to tap into it.

My second thought was to wonder if this could be at least part of what is going on with CFS.

From the onset of my wife’s illness, the symptomatic description that always fit best was that her mitochondria had a greatly diminished capacity to produce ATP. (Some doctors provide symptomatic relief to CFS patients using glutathione supplementation to boost ATP production.)

Coupling that to patients’ frequent accounts of their illness onset resembling the body’s viral defense response, I think this could be something to investigate. It may also explain why, despite symptomatic and epidemiological hints that CFS may be viral, research along those lines has so far failed.

Tossing things back in your court as a null hypothesis, how would one go about establishing that a mitochondria virus does not cause CFS? Can you think of a line of research that could probe this question?

Keep up the good work. And Alan, your punning is contagious, if not outright viral.

Tom

Austin, Texas

P.S. Vincent, I apparently missed something you said in your lectures. Several times you’ve presented a slide showing the seven viral genomes, based on their respective paths to mRNA, but the labeling circles with roman numerals only go from I to VI. Where’s the seventh genome?

Joe writes:

I listen to Science 360 radio, which broadcasts all of your This Week in ______ shows. Love them all! I am especially interested in virology, so I try to pay close(er) attention to that. Any chance you guys give an episode just based on the basics of virus replication? If you’ve already done then apologies. Also – I’m an undergrad biochemistry major/physics minor. I may be involved in some biophysics (neuroscience) undergrad research since the virus research at my university is very limited and out of my dept (biology dept is protective of their undergrad research spots). Would this cause problems regarding any chance of my getting into a virology program? Any other advice? Thanks a ton.

Big fan!

Joe

Ben writes:

Greetings TWIV chiefs,

first of all I’d like to offer congratulations to Vincent for receiving the Peter Wildy Prize (although it was, of course, only a question of when in my opinion). I have to say that TWIV is the only podcast, science or otherwise, consistently on my iPhone every week since I started listening to it in, oh my, I think 2009. Furthermore, this veritable goldmine of free and easy-to-use knowledge on your webpage is just stunning. Please continue just the way you do, I wish we had more people like you (and of course the rest of the TWIVome).

After getting this off my chest, allow me to chirp in on a tangent to your recent episode (176 – all email), where you mention it would be a good idea to have a cell version of ChronoZoom. I just love the idea, the closest thing I could come up with is – I hope you didn’t mention this on any earlier show – the Nature biology online textbook. You can register as a teacher there, they’ll give you free trial access and once you subscribe, you can have your whole class use their iOS/Android/watchamacallit devices to acces this. It’s an interactive textbook with great illustrations, animations, and films, links to related Nature articles, and, best of all, it’s updated whenever something profound is discovered in a field covered by the book.

Sorry if I sound like a Nature marketing person, I just love the idea. So, how about a digital virology textbook? I guess you’ll need a second life though. Anyway, thanks for listening, keep up the great work,

Ben

PS: Sorry, I know TWIV chiefs isn’t the most original address. I know one for your spouses, though: TWIVes. How about that?

David writes:

I wanted to point out one of the important aspects of science that is often brought up in TViW podcasts, to hopefully invoke some discussion. That point is that science is a pursuit of the truth in nature. Truth is often hidden or obscured, sometimes by the complexities of nature, sometimes by people unknowingly, and sometimes by people by design.

One important aspect of scientific investigations is the process taken to prevent us from deceiving ourselves. Science is a process, with checks and balances, partly because some truths are hard to discern. With all the different cognitive biases we are susceptible to, it is easy to be mislead by others or by ourselves. I warmly compliment all the TWiV contributors for being open to correction, a healthy attribute few seem to cultivate (especially in an election year). As Richard Feynman put it, “The first principle is that you must not fool yourself, and you are the easiest person to fool.”

David from Austin

P.S. I don’t think that check and balances are confined to science; they occur in other fields of investigation designed to ferret out the truth. For example, journalism’s “who, what, when, where, why, and how” and criminal investigation’s (at least on TV) need to establish “means, motive, and opportunity”.

A couple of cognitive bias links:

http://en.wikipedia.org/wiki/Cognitive_bias

http://en.wikipedia.org/wiki/List_of_cognitive_biases

Stephen writes:

Dear TWiV team,

With all the discussion of note taking software recently I couldn’t help but notice, and be surprised by the fact, that no-one mentioned Microsoft Onenote. I print all of my powerpoints and pdfs into OneNote and annotate around them (as seen in attached). It’s probably the most robust note taking software available, but generally has to be stored locally unfortunately. There is an option to store all of your notes on SkyDrive but the size of each page I was creating was too large for it. Although recently they increased the size allowed so I will have to test it again. You can also record audio or video into the page.

Just thought I would contribute my bit as I think it is the perfect solution for students.

[he sent twiv.tv/notes.png and twiv.tv/Cardio.png]

Amber writes:

Really interesting show, well explained and super informative. I will be back, great job!

Cale writes:

Dear TWiV,

Thank you so much for such an informative and fascinating podcast. I am a young unemployed fellow, so I spend a lot of time writing cover letters, walking the streets of brooklyn, and lifting weights at the gym. After discovering your podcast a couple weeks ago, your dulcet voices and revelatory viral musings have been the soundtrack to this strange lifestyle. After listening to TWiV 175 I started working my way through your back catalog and I’m in the mid-thirties already. I can’t thank you enough for the free educational service you provide! Thank you so much!

Best,

Cale

Tarwin writes:

Hi,

I’ve been listening to your podcasts for a few years now and, along with the Australian Science Show and Futures in Biotech you’ve now managed to teach me enough science to be able to converse, and maybe even contribute to conversations, with working scientists.

I was always interested in science, but was put off by how slow it went in high school, and ended up as a designer and programmer instead. It’s interesting how many of your listeners seem to be from tech. I think it’s partly because tech people listen to a lot of podcasts, but also because they think in similar logically creative ways. And really, when it comes down to it, playing with life is so much cooler!

Your “How to read a paper” in TWIV #169 was very useful and actually helped me track down, slowly connecting the dots, a paper that had information in it that might be able to help my housemate further his research when he thought it was at a dead end.

On another topic, how do you track how many people listen to your podcasts? The simple count of how many people subscribe through iTunes + other places may not be the best indication. Do you [technical] track the number of downloads through server logs, which would give the best idea of the actual number of downloads.

Anyway, thanks again. No need to read this on air. Just wanted to say thanks!

Tarwin (from Australia, recently Silicon Valley)

Touch My Pixel

http://www.touchmypixel.com/

TWiV 185

Ed writes:

Vincent, Dick, Rich, Alan et al.,

A couple more visual science-type picks for you to follow on from Kathy Spindler’s pick – APoD

The stunning new Pursuit of Light video from NASA: http://youtu.be/5tE5XJzZ-Rw

The MRC Biomedical Picture of the Day (BPoD): http://www.bpod.mrc.ac.uk/

I originally found both through following Joe Hanson (@jtotheizzoe, http://www.itsokaytobesmart.com/), whose blog I guess could be another pick.

Keep it up!

Ed

Multiple Sclerosis Research Center of New York

Kate writes:

Dear team-Twiv,

Firstly, thanks for all the wonderful podcasts over the years! It’s been great to regularly tune in to a more relaxed forum of academic discussion throughout my years of virology study.

I’m in the final year of my PhD at the University of Cambridge and the Institute of Zoology, and my PhD research has centred on the risk of viral zoonotic disease emerging from a fruit bat population in Ghana, West Africa.

I really enjoyed the most recent Twiv episode (183) that covered Jan Drexler’s paper about bats as reservoirs of major mammalian paramyxoviruses. That said though, there were a number of comments made on the show about a number of ‘firsts’ in this paper (e.g. first specific study of paramyxoviruses in bats, first evidence of virus closely-related with mumps in an animal host, etc) that weren’t correct.

I published an (admittedly much smaller) study in the Journal of General Virology earlier this year showing that bats host a large diversity of paramyxoviruses, including a virus closely related with Mumps.

Just trying to keep you on your toes, and thanks again for all the great podcasts.

Kind regards,

Kate

Steven writes:

Hey TWIV-dudes,

I just left a voicemail – but I’ll send this follow-up in case my message was not understandable. I think that someone out there in the TWIVaverse may be able to either answer or tackle the question that I pose.

First off, let me say: great podcast. You gentlemen are truly doing a service to the field and to society.

Let me get right into it. I’m a graduate student in virology at the University of Rochester. I work with influenza, and I just saw a great seminar this morning about gathering information from clinical/epidemiological studies after they’ve already been completed. It got me thinking of an interesting set of data that may or may not exist out there as of yet.

Are the severe (hospitalized) cases of H5N1 (bird flu) at all correlative to previous vaccination? In other words, of the 600 or so reported cases, did those individuals ever receive a flu shot? Did those who died have a higher or lower incidence of previous vaccination?

It could be an interesting question, just thought I’d throw it out there. OK, back to my experiments.

Thanks!

Steven

Don writes:

Greetings My Virome Idols,

I am a Registered Nurse with nearly 20 years in the emergency department (ED) as well as a Army Reserve Nurse Corps officer and have been a loyal listener since your team began producing TWIV. Your podcast has been a vital resource for me in both my professional realms in better preparing me for front line ED nursing as well as my military duties in the Asia-Pacific region. Till now I have not felt the need to email a question to such an esteem group such as yours, that is until this week, and I hope you can answer these concerns.

As background,I current work as a civilian staff nurse in a large military medical center’s emergency department and we were notified about a few cases of a “influenza” not covered by the current vaccine from troops returning from Japan. All reported cases have generally been mild, lasting less than a week and present with a febrile respiratory symptoms, not unlike any influenza like illness (ILI) that we see in the ED on a daily/nightly basis. The only difference is if the history includes recent travel from Japan and/or participation in the exercise in Japan over this last month. If the history does include the Japan travel and have ILI symptoms we are instructed by our infection control department to mask the patient and segregate from the general ED waiting population, especially infants, children, pregnant women, and elderly patients. These patients are to be evaluated as any other ILI patient, to include swabs for influenza virus screening and treated as would any other suspected influenza patient. Also, we were instructed that Tamiflu was to be used in “severe” cases. Our other duty in this area is to maintain a log of these patients that present to our ED and forward it to infection control office and the Command Suite as part of the daily report to the hospital commander. To date I am only personally aware of two cases.

My questions are: are any of you aware of a influenza virus from Japan that is not covered by the current seasonal vaccination and do you feel this represents a significant risk? Our measures are not different than what we did doing the H1N1 outbreak and seem reasonable. Most of our patients are active duty military and are reliable to follow instructions and comply with masking and segregation. My question here is are these measure sufficient? Since all staff are required to have been vaccinated with seasonal influenza vaccination on a annual basis as a condition of employment, how much risk does the staff have from potential infected patients and is there a number of cases seen before we raise our level of PPE use (N95 mask)? And one last question that I have always wanted to ask the TWIV Lords, after 20 years of ED nursing I have been hit with, splashed on, and exposed to more bugs than I can ever care to recall and yet I have not suffered any illness that I could remotely link to work exposure. I rarely even get a cold and I don’t recall and ILI in years. Has my immune system developed to such a state from repeated exposure in the ED or is it just my nature?

I thank you for your podcast, I greatly enjoy the weekly banter, especially the witty quips from Dr. Dove.

TWiV 184

Apoptosis writes:

A video of ‘Every Major’s Terrible: http://www.youtube.com/watch?v=LdyoGruec88&feature=youtu.be

Steve writes:

I heard TWIV 183 this weekend and Vincent’s suggestion that a listener send in a singing version of Randall Munroe’s “Every Major’s Terrible.”

Today, 05 14, I did a little research. As this blog post summarizes, there was one posted to YouTube within hours, and now there are many: http://www.mentalfloss.com/blogs/archives/126500.

I would note, however, that my e-mail to TWIV was sent on the day Munroe posted the cartoon, at 11:23 Pacific Time. I’m an xkcd fan–not so much YouTube–and had no clue about any YouTube versions until this afternoon.

By the way, I would love it if Vincent would set up an episode around his contention that science publication is “broken.” Maybe Alan Dove could discuss the embargo system from a journalist’s point of view, especially with respect to Rosie Redfield’s experience with arXiv and Science.

Forrest writes:

Hi TWIV,

I have just added another virus sculpture to my series on computer viruses.

http://www.30computers.com/CV_AdenoCD.htm

You may recall that TWIV picked up on the T9 Track Virus I did a few years ago:

/twiv/twiv-40-tamiflu-in-the-water/

This most recent sculpture is based on the Adenovirus and is called AdenoCD Virus, the 7th sculpture in this series. It is being exhibited at the Artomatic 2012 (http://www.artomatic.org) in Crystal City, just over the river from Washington, DC. This show will open this Friday May 18th and will run through June 23. Hope your listeners will stop by. There is at least one other artist there who has been generating excellent art with a virology theme, Michele Banks, http://www.etsy.com/shop/artologica.

Thanks,

Forrest McCluer

www.30computers.com

Raihan writes:

Hello TWIVians,

I came across this article about Influenza B prevalence in 2010.

Being an avid TWiV listener, i was pleasantly surprised when i saw a quote from VIrus-Guru Prof Racaniello.

‘Vincent Racaniello, PhD, a virologist at Columbia University who writes Virology Blog, told CIDRAP News that the influenza B pattern the WHO is reporting is typical. He said the two main lineages, B/Victoria-like and B/Lee-like, have been cocirculating for 25 years, with changing patterns of prevalence and geographic distribution.’

I was however a little perutrbed by the mis-naming of one of the currently circulating influenza B lineages. I would like to point out that the two main lineages are B/Victoria-like and B/Yamagata-like, not B/Lee-like.

B/Lee was the first ever flu B virus isolated in 1940 and ever since the early 80s, influenza B viruses fall in either of the Yamagata or Victoria lineages. B/Lee would fall as an outlier when compared to currently circulating strains.

Sorry if I’m being too pedantic, I learned that from TWiV.

keep up the excellent work

Josh writes:

Dear TWiV Doctors,

First a correction from my last email: I should have said Dr. Olsterholm and not Mr. Olsterholm. Apologies to Dr. Olsterholm.

I just finished watching the H5N1 Research Discussion from the TWiV link in Episode 173. It seems to me that the key question is: why is there a marked difference between the NSABB recommendation and the WHO geneva meeting recommendation? If the science is the same, is it the process that is the variable, or is it the personnel, or what else might there be?

1. The personnel: The WHO meeting mostly consisted of directors of national virology labs from around the world. You can see the list here: http://www.who.int/influenza/human_animal_interface/list_participants/en/index.html

The NSABB is quite different. It’s full of MD’s, healthcare business representatives, and lots of people who are in biosafety/biodefense labs around the country. You can see the whole list here: http://oba.od.nih.gov/biosecurity/biosecurity_voting_members.html

One voting member is Retired Air Force General John A Gordon, who was Deputy Director of the CIA from October 1997 – 2000, and Homeland Security Advisor from 2003-2004. I found him on Wikipedia here: http://en.wikipedia.org/wiki/John_A._Gordon. The NSABB doesn’t list his past achievements.

Another voting member is Marc Nance, J.D., listed as General Counsel for GE Healthcare.

Dr. Lynn Enquist, guest on TWiV 54, is also a voting member. Maybe he could come on TWiV and talk about this? Dr. Osterholm likes to say that the voting was unanimous, so I assume he cast a vote in favor. Dr. Kenneth Berns from UFL Gainsville is also a voting member. It’s too bad we don’t know anyone from UFL Gainsville who might be able to get him on TWiV……

I’m not saying anyone on the list is a “bad person”, but there seems to be a lot of non-virologists on the list. The scientists on the list are mostly from the “biosafety community”, meaning that most of them have previous experience with biosafety/biodefense committee service, such as Dr. Relman from Stanford, whose bio reads as follows:

Dr. Relman advises the U.S. Government, as well as non-governmental organizations, in matters pertaining to microbiology, emerging infectious diseases, and biosecurity. He currently serves as Chair of the Institute of Medicine’s Forum on Microbial Threats (U.S. National Academies of Science)

While there is nothing wrong with that in principle, I am concerned that the NSABB is full of scientists who are “professional worriers”, and that they might have a form of collective “intern’s disease”.

2. The process:

Dr. Fauci summed up the WHO meeting this way (http://www.1310news.com/news/world/article/331905–press-pause-who-meeting-on-bird-flu-studies-says-publish-in-full-but-later):

“It was clear that the consensus of the group was that given the clear and present danger of an evolving virus in the field, out there in the real world and the need to address this clear and present danger by research that helps to understand how viruses adapt themselves and go from one species to another … that outweighs the hypothetical risk of a bioterrorist.”

Which is exactly the point that was raised by Dr. Racaniello some episodes back. In other words, a meeting in Geneva with virology lab directors flow in from all over the world produced a result that was achieved weeks earlier by three virologists and a parasitologist talking about the issue on TWiV. However this point was not raised during the ASM Biodefense netcast. Dr. Olsterholm merely says that all sides of the issue(of publishing in full) were discussed.

Well, how do we know they were discussed? The proceedings of the NSABB are not open for scrutiny. In the video, Dr. Olsterholm clearly says that the process is closed, and the process cannot be discussed. The WHO meeting, in contrast, was not a closed process. I don’t know that a transcript is available, but from what I have seen in the press, the members were free to discuss the situation with outsiders.

So there are three examples of process. Which two processes are more similar? The two similar processes come up with the same result, the anomalous process produces different result.

3. Something else: Of course, there could be something I’m not considering. Maybe its the “jury effect”, where some members pressure other members.Maybe the normal CYA of a government committee. After all, what is the downside for them of voting to restrict? And if they don’t vote to restrict some stuff, then they might start asking themselves “why have these stupid meetings anyway?”

Also, in the video one of the guests makes the point that the Global and National reporting and intelligence systems for detecting flu are not adequate. Maybe that’s what the NSABB should be focusing on?

Sincerely,

Joshua

Ken writes:

Hello VRAD,

Thought I share with you what I just discovered and my pick for TwiV.

Wattpad – http://www.wattpad.com/

Calling itself “YouTube for ebooks,” Wattpad is a repository for user-uploaded electronic texts. The content includes work by undiscovered and published writers. Delivery emphasizes the mobile phone platform, using the free Freda ebook reader

Your long time listener and friend

Ken.

Ghana.

TWiV 183

Joe writes:

How cool is that to be listening to you all reading my emails with Peter Sandman while I am stuck in traffic.

I loved the discussion and want to send a big thank you to Michael for joining in and giving us the missing perspective of what the NSABB was thinking as they made their decisions. His efforts on the podcast are a perfect example of risk communication done well. You don’t have to have all the answers, just be able to articulate the process that went into valuing the things that created the decision in an honest way.

I apologize to Michael for my blunt technical description of them as a Nameless Faceless Government Committee, but it is an accurate description of how they were viewed by outsiders not aware of their existence prior to them making a significant decision with little public involvement in the process prior to the decision. I wrote it to reenforce the following point:

It is a critical and sometimes frustrating reality for every risk manager that when making public risk communications, if you communicate based on who you think you are things will not go well. If you communicate based on your audience’s perception of you then you have a chance to actually finish a sentence!

I was surprised to hear Michael say that there were some research that he did not think we had a right to know. I would appreciate hearing more details on his thoughts. In the world of basic science I can’t think of any that I would agree with. I agree that we should not publish the specs and construction steps for building a cruise missile in your garage, but that is different than the kind of science we are currently discussing.

Regards,

Joe

Josh writes:

Dear TWiV Doctors,

I would like to thank Dr. Imperiale from the NSABB for being on the show. It was very illuminating, and he spoke clearly about the struggles that have surrounded this situation.

He said that the WHO meeting came to a different conclusion because it was “mostly made up of flu virologists”. Isn’t that kind of the point? Experts in the field of flu virology came to different conclusion than the NSABB. Shouldn’t the NSABB defer to this group of experts on the matter? Does the NSABB dispute their expertise?

Bioterrorism is largely a fantasy of crazies and the bio-defense crowd. The real threat is Mother Nature, as Dr. Imperiale said.

Sincerely,

Josh

Mike responds:

Dear Josh,

Vincent asked a very similar question during the podcast, and I think I clarified at the time that my point was that it wasn’t surprising that the two groups might come to different conclusions. But let me answer your questions more directly.

The first thing that I want to make clear is that there is a flu expert on NSABB (Michael Osterholm) and we also consulted with other flu experts as we were discussing the original manuscripts last fall. Thus, we did not make our first recommendation in a vacuum. Second, I do not dispute the expertise of those who participated in the WHO meeting. However, they have not spent the past seven years together discussing the dual use issue, as NSABB has. NSABB’s expertise is much more broad, including microbiology, infectious diseases, biosafety, public health, veterinary medicine, plant health, national security, biodefense, and scientific publishing. One of the things NSABB has been stressing is that the scientific community needs to be more engaged in discussions of dual use.

Regarding your statement about bioterrorism being “largely a fantasy of crazies and the bio-defense crowd,” I strongly disagree. I think the Native Americans who were deliberately infected with smallpox by the British in the 1700’s, or residents of The Dalles, Oregon, who were poisoned by the Rajneeshee sect with Salmonella in 1984, or the relatives of those who died from the anthrax letters in 2001, among others, would also disagree with you. Bioterror is very real, and groups like Al Qaeda have publicly expressed their desire to use it. That is not classified information: it is freely available. Here is an example that was just reported a week ago by CNN:

http://security.blogs.cnn.com/2012/05/02/from-the-grave-al-awlaki-calls-for-bio-chem-attacks-on-the-u-s/

Best,

Mike

Kim writes:

Hello TWi hosts!

I’m studying the bachelor program in biomedicin at Karolinska Institutet, Stockholm. I found these lovely podcasts (TWiV/TWiM/TWiP) during our course called “Infection & immunology”. We were working with Semliki forest virus and supposed to do calculation involving the infected cell cultures, to which I found help from your website. I then discovered the podcasts, which I used for support when studying for the exam. From that day I was hooked. I’ve continued to listen to your podcasts, both old and new, and I absolutely love them.

Now for my question! I’m curious to what your opinions are on pre-postdoctoral studies (meaning bachelor, master and PhD studies) and their importance for someone who is pursuing and dreams about a career in research. As an example I can use myself, because I should soon choose how to continue my studies. I’m not sure if the structure is the same in the States as in Europe, but the crossroad I’m at is which master program should I choose that would help me the most in continuing my studies. I’m weighing between a program in microbiology and a program in biomedicin, both resulting in a master’s degree, and wondering what implications might this decision have for my future. I feel that I would love to study only microbiology for two years, but I also feel that it might give me a “tunnel vision” in a way because I would only focus on one thing. In contrast, biomedicin would provide a wide knowledge of many fields, but less specific and in depth. Do you think this decision really matters in the end if I aim at a career in research. I’ve heard that ones postdoctoral work is in a way the research which defines one the most.

Please do tell us about your own studies and how you feel they shaped your future resulting in a career in research or something else (depending on which hosts are present while reading this). Thank you very much for your answer and keep up the good work! And the weather has been around 5 Celsius for many weeks now, so almost summer!

Best regards,

Kim

Todd writes:

Even though it’s not something you’ll likely put on your resume, but I just wanted to congratulate Vincent on being quoted in Maxim magazine for clarifying that, contrary to the TV show Lost, you cannot disinfect a wound with vodka due to less than 66% alcohol content. (Channeling Alan) You could have enhanced your viral sex appeal if you had also mentioned that research shows cleavage is utilized in some viral reproduction.

Tyler writes:

Just as a quick FYI, I wanted to let you know that I will be staying at the Dengue Branch in a permanent position once EIS is over in June. One factor that motivated my bosses to find the money to keep me here was my TWiV interview, which garnered a lot of attention for the Branch in a variety of capacities. I therefore wanted to thank you again for offering the interview and helping to make it such a positive experience.

Peter writes:

One minor point on episode 181, we’ve seen a few cases here in the UK where sheep farmers have picked up skin lesions on their hands after vaccinating their sheep against ORF. Another route of infection to add to your list. Of course here in the UK parapoxviruses are all about the poor old red squirrel.

All the best,

PB

HCV Group : School of Immunity and Infection :College of Medical and Dental Sciences : University of Birmingham

Matt Evans writes:

Hello Vince and all the TWiV hosts,

I am interested in adding people to my lab and it occurred to me that there may be no better place to find motivated young virologists than TWiV! If you think it would be appropriate, please post this on your website or even read it on the program.

My lab studies the hepatitis C virus and how host factors influence entry and replication of this virus in host cells. I am currently looking to hire a postdoc with a strong research track record. I am also interested in hiring a technician, who will help maintain the lab and conduct their own research projects. I am sure that successful applicants will find the Department of Microbiology at the Mount Sinai School of Medicine in New York a terrific place to study viruses.

Those interested in applying can find my contact information on my Mount Sinai webpage: http://www.mssm.edu/profiles/matthew-j-evans

Many thanks,

Matt

TWiV 182

Joe writes:

Vince, here is the text of my post on Peter S site. I was disappointed in the quality of his article as I have much previous experience with his work and see him as the “David Baltimore of Risk Communication”. If you could get him on as a guest you would enjoy the discussion. He reminds me of D3 in his ability to tell a story.

Regards, etc

Joe

Peter, while I have the greatest respect for you and have been to trainings by yourself and Vincent Covello in years past, I have to tell you that this article is very flawed both in the “facts” used and in the conclusions.

About 5 years ago I did the work to prepare my global organization for responding to a potential pandemic based on my concerns over H5N1, SARS and a few other pathogens. At that time I did the work to get as complete an understanding of the state of the science that I could achieve with my background in Chemical Engineering and Environmental Science. Within a few years the public discussion caught up with risk management trade’s discussion on pandemics and we saw serious resources put into preparedness planning at the international, national and local levels. We have relatively robust systems in place and are working to improve the major deficiencies in prediction, vaccination and control.

The research and the researchers you are unhappy with have been an integral part in trying to get the answers risk managers like me need to make good decisions related to these preparation. Their emotional response to the criticism of a faceless unknown committee is very understandable to me. Their efforts to remain professional is to be praised and their lack of sophistication regarding risk communication seems to be something they are working to rectify.

I would argue that the Decide, Announce, Defend strategy you describe better describes the NSABB’s approach than the scientists. And the target of their decision was not a few papers but the fundamental process of scientific communication among peers by publishing finds for peer review. Scientists value this in a way equivalent to the 1st amendment of the US constitution. To me their outrage is appropriate and reasonably targeted.

WRT the facts:

We know the 60% number is not accurate in the way you used it. It is the % of those who sought hospital care that died. The number of people infected is certainly much larger and there are good studies that indicate that this flu is currently in or near the typical flu Case Fatality range of 0.1%- 2%.

This flu strain is not exceptional in its lethality as you characterized it. Ebola, Nipah virus, HIV, Hep B, SARS, and many other pathogens are very similar to it or worse that it in virulence.

There is little mystery in how the 4 BioSafety Levels of protection are determined for a given pathogen.

1 = not a human pathogen,

2 = human pathogen that is not airborne transmissible, (e.g.,HIV, Hep B)

3 = human pathogen with life threatening disease that is airborne and for which we have treatment or vaccine (e.g., flu, yellow fever)

4 = human fatal pathogen possible airborne transmission with no known treatment

The BSL system had been incredibly successful at stopping lab acquired infections and loss of containment not withstanding unproven speculation about the source of H1N1 (note that it has an excellent reservoir in pigs where it experiences little evolutionary pressure)

These experiments are not as unusual as you suggest. The value in publishing them is in accelerating our ability to develop an effective treatment or vaccine. To build our defenses against a natural or unnatural outbreak. Their work is totally reproducible by any competent biologist with a supply of ferrets and virus (both readily available).

My view is the NSABB did not understand the history of research in this area, made a knee jerk decision to ban the details and were caught by surprise when knowledgeable people protested the impacts of their decision on all scientists.

Warmest Regards and please keep on with the business of improving our risk dialogs.

Joe G.

EH&S Manager

Peter Sandman responds:

Thanks, Joe, for your kind remarks about my work and your thoughtful ones about upcoming risk communication challenges. And thanks for sending me your critique of my Genetic Engineering & Biotechnology News piece on the H5N1 publication debate.

I’m drafting a response to the latter, which I hope to have ready to post with your comment in a few days.

For the sake of clarity: I have posted three commentaries on this issue so far. (This Guestbook comment-and-response will be #4.) Here they are in chronological order:

“Bird flu risk perception: bioterrorist attack, lab accident, natural pandemic” (http://www.psandman.com/gst2012.htm#NSABB) – a Guestbook entry posted on January 19, 2012.

“The H5N1 Debate Needs Respectful Dialogue, Not “Education” or One-Sided Advocacy” (http://www.psandman.com/col/WHO-H5N1.htm) – the article TWiV discussed, really an email to Lisa Schnirring of CIDRAP News, posted on February 17, 2012, which she drew on for her article (http://www.cidrap.umn.edu/cidrap/content/influenza/avianflu/news/feb1712meeting.html) of the same date.

“Talking to the Public about H5N1 Biotech Research,” (http://www.psandman.com/articles/H5N1-1.htm) – the article you read, submitted to Genetic Engineering & Biotechnology News [ital] on March 18, 2012. (The version the magazine published [make “version the magazine published” a link to http://www.genengnews.com/gen-articles/talking-about-h5n1-research/4067/] on April 15 under the same title is somewhat shorter.)

All the best.

–Peter

P.S. I’m not sure whether it makes sense for me to participate in a future TWiV netcast or not. I’d be interested if the focus were on risk communication issues raised by the controversy … not the technical issues where the moderators are experts and I’m a novice. (Even if I were right – or more likely half-right – on a technical point, they’d still outrank me and could still out-argue me.) But given that the papers are headed for publication now, a conversation about the risk communication implications of the mooted publication debate would probably seem pretty peripheral to the TWiV audience, I think. Still, I’d be open to an invitation of the three moderators think it makes sense … and I won’t feel slighted if they think the moment has passed.

Joe responds:

Peter, it is interesting to me as we continue this dialog (and now that I have read the actual paper discussed on TWIV) that it is a perfect example of how much people can disagree even when given the same facts!

I don’t think the work that has created the ruckus is that different than similar work going on all over the world with a variety of organisms, many that I find much more concerning than H5N1. I must admit that I don’t watch TV news so I may have missed some of the drama. My view at the time was that the researcher, Dr. Fouchier, created the problem by announcing to the media that “he had created the world’s scariest virus” (assuming the facts I saw are accurate). I later heard him talk on the TWIV episode in Dublin and he seemed much more circumspect now that he has experienced some “live fire” media training. Now that I know he had to pre-mutate the wild virus to give it a starting chance to passage through the ferrets, I find the risk of a pandemic lower not higher than before. What he did actually proved just how high the natural barrier is between H5N1 and mammals.

There is a lot of research being done in BSL 3 and 4 labs that could be much more worrisome than this if it was not done with the extreme caution and rigid rules of the BSL 3 and 4 labs. Since one of my jobs is to coordinate with the safety staff that run the BSL 3 and 4 labs in the USA to allow our field service engineers to come out and repair our instruments in their labs I know just how seriously everyone takes these rules. When you say the virus is stored in a lab, that does not quite conjure up the reality of how they are stored in a double sealed container in an isolation system within at least two other isolation systems (BSL 4 labs live within a BSL 3 lab that usually are attached to a BSL 2 lab).

Has there been a lot of media coverage of angry scientists on this issue? I haven’t seen it but would not expect to if it does not show up on the web. I ask because I would not characterize most researcher in the biotech world as dismissive of public concerns. These are in fact the same folks who volunteered to put on the Asilomar conference when folks were scared of genetic engineering in the 80’s. I can’t think of many branches of research that took what could have been considered uninformed fear more seriously.

One part of this debate that has baffled me is the focus on not publishing this kind of work when that is exactly what we need to develop realistic response plans. The irony of it is that I would bet the eternal box of doughnuts that there was much scarier work being done 10-20 years ago to weaponize smallpox that was never published because we were not supposed to be doing it. You and I did not have a need to know! They are not saying don’t do the work just don’t publish the results! All the (minimal) risk with none of the valuable gain.

Regards

PS. you would have fun on the TWIV podcast. Actually the discussion that would be very worthwhile would be on how to better communicate the need for vaccines to an ever more confused public. A great venue to reach the scientists and doctors interacting with people on this critical issue. The hosts spent many episodes trying to get the science clear on CFS and the purported links to the XMRV virus as it was breaking news the last 2 years.

Joe

EH&S Manager

Josh writes:

Dear TWiV Doctors,

I have a suggestion for a listener pick of the week: Dr. Paul Offit’s course on Vaccines from UPenn on Coursera. It starts in June and is free. It does not appear to be an technical course, but rather a general examination of the history, science and use of vaccines. As such it might of more interest to lay-people than people in the field. My assessment might be inaccurate, however, since I have not taken it (yet).

https://www.coursera.org/course/vaccines

Sincerely,

Josh

TWiV 181

Spencer writes:

I would like to propose the book:

Netter’s Infectious Diseases, 1e as a listener pick of the week.

The book, filled with great explanations, is beautifully illustrated by the late Frank Netter MD, a pioneer in medical illustration. As a student, one of my classmates at Mount Sinai actually had Dr. Netter as a cadaver. Dr. Netter taught us so much in life as well as after! The sections on parasitic diseases are particularly well done.

Sincerely,

Spencer MD PhD

Richard writes:

Hi Vincent and other hosts!

I have no silly questions for you this week, but a book that I found interesting.

Germs, genes and civilisation: how epidemics shaped who we are today.

By David P Clark

Thanks again for the series of podcasts, that I enjoy learning from each week.

Regards

Richard

Andrew writes:

Good [insert appropriate distinction regarding time of day you receive this] gentlemen of TWiV,

I’ve been an off-and-on listener to TWiV for what must have been before 2009 in the middle of my undergraduate years. This podcast serves as an example of the power of the medium to deliver focused higher-level discussion on topics too complex to survive on traditional broadcast media but still casual enough for the non-scientist. So thank you for your excellent service to us, the listener!

The question/concern/comment I’m writing about is this: Graduate School is Scary. I graduated from a local state school with a BS in Biology in 2010, and have been out of school for just under two years. I’ve maintained some (probably about 5-10 hours a week) of activity in the population genetics lab I worked in prior to my graduation. Some family issues kept me tied to the area and reluctant to apply to graduate school but recently those issues have resolved themselves and now I find myself looking to take the next step. This is very frightening, and I find it difficult to proceed. How do I find what Masters or (preferably) PhD program is right for me? Am I doomed? What do I do if the program best for me doesn’t think I’m best for it? It seems too late in the year to apply to anything? Most programs have closed applications by now and those that haven’t have disclaimers stating that funding is usually assigned already. Should I bide my time and wait? In the mean time, I’m currently applying to the IRTA Postbaccalaureate Training Program which seems like a great program to get into in order to help bridge that gap between undergrad and PhD (and may even deserve a mention on the show: https://www.training.nih.gov/programs/postbac_irta ). Any advice on how to proceed when caught in this quagmire would be greatly appreciated and would likely help any listener also caught in the same post-undergraduate-pre-graduate morass.

Thank you, whether you read this or not, your podcast has been a huge influence on me. Please, never stop.

P.S. I forgot to actually include the field of study I’m interested in, because I meant to move it around, then forgot to reinclude it. My longstanding interest in genetics managed to fuse and include virology, and so ideally I’m most interested in virology (hence looking for TWiV’s perspective) with a focus on evolution and genetics.

Jim writes:

Hi Vince,

Last November you had Science360 Radio as a TWIV pick. There are now over a hundred program links there. That provides a concentration of material you can point folks towards to more easily find what they want. I hear many podcasts from these places that are good, but some sites always stand out, like TWIP/V/M. Others periodically have great shows or a segment of a digest, and some have a huge number of past programs. So if you have an interested listener, I don’t know where you send them, especially if their time is limited, such as a teacher who wants to use certain subjects.

I’m trying a blog describing selected items culled from 60 or more podcasts each week thinking it might be a way to make better podcasts easier to locate. No feedback or comment has occurred after 16 entries over four months, a short period considering the probability anyone is even looking. I now suspect blog material is read more frequently on smart phones and my efforts are too wordy for small screens, so will begin producing shorthand-type entries. It does a far better job of offering material than an alphabetized list of podcasts on my hard drive. This doesn’t address all your TWI(*) efforts, especially as their numbers increase, and only a few of them are included in this blog.

Anyway, if you contact anyone to suggest an article about use of podcasts in schools, the attached list of 92 rss feeds with podcast names might be of use. In addition, this link about listening faster might be of use, too, in light of Kathy Spindler’s comment about finding time to hear your episodes. The blog, Media Mining, is included should anyone have an interest in that approach. Suggested improvements are welcomed, of course, to include ditching it for some other approach.

Oh, I enjoyed your descriptions of daily activities; all time well spent!

Regards,

Jim

Smithfield, VA

Stephanie writes:

Dear Twivers,

I was a bit shocked when a listener wrote in last week and requested that you guys to avoid the subject of evolution in order to avoid offending anti-evolutionary Christians. I understand that, in order to reach the largest audience possible, it is important to be politically correct. But, is it even possible to discuss papers in the field of virology without understanding viral evolution? Why do viruses become resistant to drugs? Why does a virus tend to be less pathogenic in long term hosts? How did viruses develop so many ways to subvert host immune defenses? This is a sensitive subject to be sure, but this subject is something that just about every teacher of biology must face at one point. I look forward to hearing how you guys respond to this issue. You TWIVERs are role models for the scientists and educators that do not practice communicating science to a large, diverse audience on a weekly basis.

Horatio writes:

A brief comment on rabies: the genotype 1 rabies virus usually sustains itself in an endemic cycle in different carnivores according to geography and species composition. Bats may carry genotype 1 but are not needed as reservoirs; however they are reservoirs of the specific bat genotypes, which may cause disease in various animals and humans. Fortunately, the basic reproduction number of rabies virus is low, primarily due to the particular mode of transmission, restricted tissue tropism and long incubation time. Let’s hope that the path to a putative, aerogenically transmitted virus is long and with many obstacles.

Erica writes:

Hi Team TWiV!

I just wanted to write in and let you know that you did indeed discuss miR-122 and HCV in a previous podcast as Rich suspected–it was episode 97 with my PI, Peter Sarnow. Not only is Peter a fantastic mentor, but he is a pioneer in the field of virology, and his episode on your show is one of my favorites. I highly recommend it to anyone who is interested in learning more about miR-122 and HCV.

Thanks so much for a great podcast!

Rohit writes:

I was pleasantly surprised to hear our (miR-122 & HCV) paper discussed on Twiv #180. We are really glad to know that the TWIV crew liked our study. Thanks for discussing our paper.

Currently, I am a postdoctoral fellow with Dr Benjamin tenOever in the Department of Microbiology at the Mount Sinai School of Medicine where I am trying to further develop the novel technology of use of host miRNAs to engineer a live-attenuated influenza vaccine. This technology was demonstrated earlier by Jasmine Perez in the tenOever lab [http://www.ncbi.nlm.nih.gov/pubmed/19483680].

I did my PhD with Dr Stan Lemon while he was at the University of Texas Medical Branch (UTMB) at Galveston, TX. Some of the initial experiments of the PNAS manuscript were actually carried out in the Lemon lab when we were located on the 5th floor of the Galveston National Laboratory, where you are headed sometime soon to do a TWIV episode.

I thought that I would answer some of the questions that came up during the discussion of the paper. In addition to its positive role in HCV replication, miR-122 also regulates cholesterol metabolism in liver. Knockdown of miR-122 significantly reduces serum cholesterol levels in mice as well as non-human primates. Thus, miR-122 is also an attractive drug target for cardiovascular diseases. However, certain liver cancers are associated with lower miR-122 levels suggesting that long-term knockdown of miR-122 might have some side-effects.

Location of miRNA targets in 5’UTR by itself is not enough to change a miRNA from a “repressor” to an “activator” of gene expression as there are examples where miRNA targets located in 5′-UTR of mRNAs down-regulate gene expression. Thus, miR-122 effect on HCV 5′-UTR seems to be unique so far. However, there must be other such examples out there that are yet to discovered.

Allan was right in pointing out that RISC, as the name RNA-Induced Silencing Complex suggests, is a complex of multiple types of proteins. Argonautes are the central and canonical components of RISC. There are 4 argonaute proteins in the human genome, argonaute 1-4. Ago-2 is the best studied one and is the only argonaute with a slicer/endonuclease activity that is used to cleave the target mRNA when there is perfect complementarity between miRNA/siRNA and its target.

Thanks

Rohit

Stephen writes:

I’m a new subscriber to TWIV, and just began with #180. Richard Condit’s comments on polydnaviruses and wasps was fascinating, and I will follow up on that.

A few comments:

1. Broken link: “Viral and wasp genes involved in symbiotic replication (J Virol)” http://www.ncbi.nlm.nih.gov/pubmed/22238295

2. braconid wasps are parasitoids, not parasites. Parasitoids kill the host.

3. The layers of complexity involving parasitoid wasps are sometimes even deeper. Here’s a photo I took by accident while shooting some grasshoppers (Nisquallia olympica http://onh.eugraph.com/insects/orthop/nolympica) I casually study in the Olympic mountains. I’ve appended a comment from bugguide.net, to which I contributed a crop of this photo.

Brachymeria tegularis…

These are hyperparasitoids of common grasshoppers (through sarcophid and tachinid flies). More commonly found in western states. Great find.

See reference here.

… Ross Hill, 12 September, 2011 – 4:32pm

http://bugguide.net/node/view/575501

So the flies parasitize (or parasitoidize) grasshoppers, then Chalcidid wasps lay an egg on the grasshopper. The larva of the wasp then finds the larva of the fly and parasitoidizes it.

I have to wonder how much of a role viral genes play in all of this.

TWiV 180

Rohit writes:

Hi Dr Racaniello,

I am a long time listener of TWIV and really enjoy the informal scientific discussions. I listen to TWIV while working in the lab and am trying to catch up on TWIM and TWIP episodes too.

I have been dilly-dallying on the idea of writing to you for a while now as the paper that I am suggesting is in a way self-promotion. However, I thought that you may find this study interesting as it presents a very interesting example of a virus (HCV) using a liver-specific miRNA (miR-122) to protect its genome from 5′-exonuclease-mediated degradation (attached paper). This paper not only describes a novel way used by an important human virus to slow down the rate of viral RNA decay but also adds a novel mechanism of action to the repertoire of mechanism of action of cellular miRNAs. Usually miRNAs down-regulate expression of target genes by decreasing translation and/or enhancing the rate of degradation. However, HCV has devised ways to use miR-122 to both increase its translation, protect its genome from 5′-exonuclease-mediated degradation and potentially prevent detection of 5′-triphosphate containing viral genome by the cellular immune response.

I enjoy all three podcasts and look forward to many more episodes of them. Thanks for keeping me up to the speed on some of the interesting developments in virology and microbiology as well as fascinating discussions on parasites.

Rohit

Postdoctoral Fellow

Department of Microbiology

Mount Sinai School of Medicine

New York NY

Tanel writes:

Dear twiv team,

Very nice of you to have read my letter. Boston marathon is history for this year. Despite of the crazy heat, I made it to the finish. Took me much more than I expected (final time 3:26:39) but still, it’s done. Was great! Ahead is a new running season with new goals in my mind and new twiv episodes to spice up the time in running shoes.

Thank you again for your time and effort!

Best,

Mr. Tanel

(a typical name for boys born around 1985 in Estonia 🙂 )

PhD student

Department of Virology

University of Freiburg

William writes:

Dear TWiV Doctors,

I stumbled upon your webcast this morning, and as an aspiring virologist I am looking forward to going through the archives. I particularly enjoyed this episode because I work for Dr. Kathy Hanley at NMSU doing research into dengue virus-mosquito interactions, and my eventual career goal after I get my PhD is with the PHS. An interesting thing about dengue that was outside the scope of the interview is that dengue also has an extant sylvatic cycle in both Southeast Asia and Africa. This is important because it could serve as a model system for other as yet un-emerged zoonotic viruses, as well as currently emerging viruses (chickungunya being an excellent example). Furthermore it is a potential complication should an effective tetravalent vaccine be approved for use, as these sylvatic viruses are entirely capable of spilling over into humans, and have the same epidemic potential.

It will be an interesting year for arboviruses with the early onset of the mosquito season across much of the country, along with the presence of dengue in the Keys, as well as West Nile.

Keep up the good work

William

P.S. I am not ashamed to admit that I carry Principles of Virology around with me on a daily basis.

Jesse writes:

I don’t know if you remember, but we met briefly when I was at Columbia visiting Ian Lipkin’s lab two summers ago. At the time I was a postdoc with David Baltimore. I really enjoy your Virology Podcast, and listen to it whenever I get a chance.

I have to say however, that as an influenza virologist I’ve been a bit disappointed in how you and your co-hosts have treated the H5N1 research debate. I think this issue is more complex and deserves more balanced consideration than almost all commentary, including your own, has given it. I thought of this today when I read an essay by Peter Sandman (which I have forwarded below) on the topic. The essay is the most intelligent thing I have read about the debate, and I think it has some good suggestions. I know you and your podcast represent one of the most respected voices in virology (certainly I respect it a lot!), so I thought I would forward along the essay.

Thanks,

Jesse

Assistant Member, Basic Sciences Division

Fred Hutchinson Cancer Research Center

http://labs.fhcrc.org/bloom/index.html

Josh writes:

Hello future, Vincent, Allan, Rich, Dickson, and all other present contributors. I started listening to TWiV in November 2011 and am up to episode #95, so hello from 2010! I would like to express my deepest gratitude for the work that you do and the education you provide to the listener. I can say that this show has singlehandedly assuaged my fear of vaccination, which was built on hearsay and fear mongering. I would like to ask a few questions and share a video I’m hoping at least Vincent will like.

TWIV #92 discussed plant viruses making plants resistant to drought and other adverse conditions. Is it possible that there are similar viruses conferring resistance to people living in extreme climates, such as Saharan Africa, or the Arctic Circle? Or for that matter could there be microbes, or parasites that help people in these extreme climates manage to live there? For example Dickson has mentioned that the Inuit and Yupik peoples are nearly 100% infected with toxoplasmosis and perhaps other meat borne parasites. Is it possible that these people have given an advantage in dealing with the extreme conditions present in the Arctic Circle by the viruses, microbes, and parasites present there?

On a different note rabies seems to have been around humanity and with humanity for a long time. I realize that the natural host for rabies is bats, however my question is more homo-sapiens-centric. Does its current disease cycle in humans maximize transmissibility? If it does how do hydrophobia, manic mood swings, and whatever other signs and symptoms exist aide in transmission? If not, why hasn’t the virus mutated to a form that can better transmit in humans? If it doesn’t transmit well from humans, could the lack of mutation be because of the limited amount of human borne infections comparative to viruses that mutate much more quickly to maximize transmission?

My third question is related to viruses used to construct things. I think you guys mentioned that viruses can be used to construct batteries. Could a virus be used to construct the most basic structures inside a cell. As an experiment would it be possible to create any, if even the simplest, structures that make up a cell using viruses as the building agent? I realize this idea leads to a “were viruses the root of the tree” type of argument, but frankly I’m not as interested in that question.

As for the video, Vincent mentioned that he liked the Abbot & Costello skit “Who’s on first?”. This is a modern rendition of that skit that I think uses a really clever twist. I should point out that I do not watch sports so I have no idea how current or valid the content is.

http://comedians.jokes.com/slovin-and-allen/videos/slovin—allen—abbott—costello

Thank you all for your excellent work, and ditto to Rich on what to tell everyone if you had 5 minutes to talk to them. I apologize for the length of this email. I generally save up questions until I am overwhelmed and need to write. Please feel free to read or omit whatever you feel like.

Sincerely,

Josh

TWiV 179

Ebrahim writes:

Dear Dr. Racaniello

I was watching the conference in Dublin and I wanted to thank you for sharing my e-mail with the people in the panel, since I saw how nice it was for me to reach the specialists with that ease through TWIV.

As a footnote actually my name is Ebrahim not Laurence 🙂 but anyways thanks again!

Kind Regards

Josh writes:

Dear Dr. Racaniello,

Thank you for reading my email on the air on TWiV 178. It’s always nice to be included on my favorite podcast, even if you guys did disagree with me.

Would you mind an outsider’s perspective on the situation? And although TWiV is my favorite podcast, I am an outsider: I’m not an academic, and I don’t know any of the people involved.

I am apprehensive about the entire role of the NSABB, and fear that the biological community will soon be subject to the same levels of restriction and classification that currently affects the physics community. I think that in almost every case, things that fall into the category of classified information are almost always done for reasons that have nothing to do with the science, and everything to do bureaucratic nonsense. Restricting information about nuclear weapons, for instance, hasn’t prevented many countries from acquiring them.

Which disappointed me when you read my letter on TWiV, not because you disagreed with me but because I wonder if you are seeing the larger picture. I agree that it should be about the science, but it’s not. Once you remove the scientists(and there are lots of non-scientists on the NSABB) from the equation, it’s about politics and the bureaucrats. So they are going to either restrict the information or they are not. If they do, we agree that this is a bad thing. If they don’t, this is a good thing. In this instance, it’s kind of a zero-sum game.

A game that I believe TWiV played a large part in winning, because week after week you applied pressure to the scientists and other members of the NSABB by calling them out on their nonsense. It’s one thing to be rebuked for your actions behind closed doors, and quite another to be publicly reminded that you are not following the science by your peers. You had an issue that you are passionate about, you skillfully applied public pressure, and your side won the day. That’s not only how you play the game, it’s how good policy wins out over bad policy.

The next policy fight that is coming is that those people on the other side want to change the entire scientific publishing system in the US and Europe. They want to have a system where those people “on the list” get the papers, and everyone else does not. Those people “on the list” will not be able to discuss it either. Anthony Fauci said as much on that NPR story. It’s not only bad policy, it’s bad science. TWiV can either be in the middle of this policy fight, or it can be on the sidelines. I know what I would prefer.

I know it’s distasteful. I know you don’t want these public dust-ups. But what choice do we have? If you don’t engage, then they will not be any opposition to the plans. And that’s an outcome I don’t think our country can afford.

Sincerely,

Josh

P.S. On a personal note, TWiV and your online virology course inspired me to sign up for MIT’s new online course offering, 6.002x, Circuits and Electronics. It’s week 5 and so far, so good. The math is hurting me since I haven’t had calculus in 20 years, but I’m mucking through it

Tanel writes:

Dear Twivoners (twiv + marathoner),

I’m a grad student from Freiburg, Germany (originally from Estonia though), who has been listening to twiv as long ashas been running. On Monday 16th I will run the Boston marathon and no matter how it goes, I would like to use the opportunity to thank the twiv team for the support throughout the training season. Research and graduate studies can often be frustrating and running has been a way to keep a clear mind. Running 6 times a week and between 8 to 30 km a day, means quite a bit of time in running shoes.

Twiv (but also twip) has made those hours also entertaining and educative!

I’m sure there are many researchers in running shoes and maybe even those who will join me on Monday in Boston. Good luck fellow twiv listeners and marathoners!

All the best,

Tanel

PhD student

Laboratory of Prof. Stäheli

Department of Virology

University of Freiburg

Maximilian writes:

Hello TWIVers!

I discovered your netcast today, and I am hooked!

I am currently a pre-frosh at Duke University’s Pratt School of Engineering, with an intended major in Biomedical Engineering. I have two questions for you, which I’ve been thinking about for the past few weeks while I finalize my intended major/double major.

1) Is there a possibility of working on viruses/immunology if I were to focus on protein engineering? I ask because my first love in biology was virology/immunology and that love has always competed with my more prevalent interest in BME.

2) Would it be more prudent to double major in Chemistry (conc. on biochemistry) or Biology (molecular/cellular) if I want my double major to focus on my interests in virology and immunology?

Thanks so much,

Maximilian

Thanks again

TWiV 178

Josh writes:

Hello TWiV Doctors,

Two short things:

1. You probably already heard the TWiV shout-out you got on NPR’s Morning Edition on Friday, March 30th. It’s here: http://www.npr.org/2012/03/30/149664035/policy-on-high-risk-biological-research-tightened

2. Since the NSABB caved (and it was more like a rout) you can put one in the Win column against the forces of darkness. I know you are scientists, but high-fives are appropriate.

Ayesha writes:

Dear TWIValians,

I submitted my thesis last Monday and wanted to share Acknowledgements page with you. Please skip to end for the relevant acknowledgement.

Cheers everyone, you made a big difference to me!

Acknowledgements

I am extremely lucky to have many people to thank. Thanks are due to:

Dr Julian Naglik for his help, his patience and consistent encouragement throughout this process. He is truly a remarkable person and supervisor all around! I have been very fortunate to work with his group on this NIH funded project with further support from King‟s College for the Overseas Research Studentship (ORS).

Dr Celia Murciano for advice on figures, experiments, extensively proofreading the thesis, for performing last minute Luminex assays and conquering troublesome westerns. She is a giver of love, kindness and understanding that helped me get through.

Dr David Moyes knows everything about everything and is always willing to chat about it with anyone. His generocity and advice were always welcome especially for anything to do with fungus, qPCR, microarray, the thesis and computer savvy.

Dr Arinder Kohli for the Cat 3 training, most HIV techniques and so many moments that now make for very entertaining stories.

Manohursingh Runglall for his friendship and sharing his fantastic lab know how.

Dr Chengguo Shen and King‟s College Genomics Centre for performing the labelling, microarray protocol and producing the gene list for analysis.

Dr Simon Jeffs for UG21 protein and antibody for its detection.

Carlo Scala for performing p24 ELISA for my samples alongside his own and Professor Charles Kelly for ordering ZM96 from NIBSC on my behalf.

Dr Trevor Whittall, Thomas Seidl, and Dr Yufei Wang (from Professor Tom Lehner‟s lab) for help with flow cytometry, experimental design and trouble shooting.

Professor Stephen Challacombe for his wisdom, good humour and gentle guidance. I greatly appreciate the time he spent with me.

To Dr Abigail Tucker my postgraduate coordinator.

To my parents, Anne Senécal-Islam and Dr Shamsul Islam for encouragement.

To my husband Angel and daughter Aurora, who allowed me to finish this degree. It would not have been possible without their full cooperation and help.

Thanks are also due everyone at This Week in Virology (TWIV) podcast for re-infecting me with enthusiasm for science.

Johan writes:

I love This Week in Virology, and I just wanted to give my appreciation of the latest episode. So long time since the last video episode!

Thanks

Johan

Sweden

Sasha writes:

Hello, symbionts and hosts of TWiV!

I am a high school sophomore (from western Maryland,) and am writing to you for the first time in the three (or four) years that I’ve been listening to you. Admittedly, by now, you all seem like old friends whose voices would be sorely missed if I went a day without hearing a fascinating and entertaining conversation about viruses. What inspired me to write might come as a bit of a surprise, but I’ll get to that in a moment.

On TWiV 142: Viral oinkotherapy, you discussed a paper involving microfluidics. The details are a bit hazy to me, as I often listen to TWiV while preparing for bed, but I remember the concept very clearly. Having always been interested in circuit design, and since my discovery of TWiV, virology, it occurred to me very recently that microfluidics and microarrays, (and I’m not quite sure which is a subset of the other,) are a very nice marriage of my two primary interests.

That being said, perhaps in the future you could spend a bit of time on some papers regarding those topics. (I’d also be interested to hear your thoughts on them!) It seems to me to be a very promising emerging field, particularly for use in fast-testing and analysis where relatively little sample material is available. I also found a blog/website by the name of Microfluidic Future, which I suppose will be my listener pick of the week.

Now, on to the less virus-related, but still interesting part, which caused me to write in the first place. Back in 2008, a comic was posted on xkcd.com. It detailed a method for determining a number of random locations, at least one of which was guaranteed to be within a relatively small number of miles for any given location. This was termed “geohashing,” and was imagined as a means to select a location for, say, a local meetup. There is a relatively active community centered around this concept, and they’ve demonstrated that it is quite possible for people to use these random locations for meeting places.

This could be relatively easily applied to meetings surrounding TWiV! Using this tool, anyone can find the geohash for their latitudinal and longitudinal zone. If some members of your wide and ever expanding audience became interested in this, we could begin to plan meetups at these locations. After all, networking is what viruses are all about, isn’t it?

Anyway, thank you for reading my lengthy and geeky letter, and I hope you enjoyed my comments!

Alexander

(alias: Alexander help I’m trapped in a username database)

Lawrence writes:

I just wanted to express my appreciation for your podcast, and to tell you that I find your discussions fascinating. I am trained in engineering, but have a wide range of interests in all things scientific and am now turning my attention towards microbiology. Listening to your discussions of scientific publications and hearing the scientific mindset at work is soothing balm to my psyche in our world awash with banality, scientific illiteracy and anti-science. I keep a notepad with me as I listen and jot down words with which I am unfamiliar, and spend time afterwards researching their definitions which opens up new horizons and broadens my perspective in areas that I likely would never have encountered were it not for your podcasts. Thank you all very much for your time and effort.

Paul writes:

TWiVarians,

I just thought you might be interested. I donated blood today and as I was signing in, I had to read a paper that would disqualify me if I had ever be diagnosed with Chronic Fatigue Syndrome. The most interesting part of the paper was that it said a virus called XMRV was linked to CFS and since they didn’t have a valid test for XMRV, I couldn’t donate if I had been diagnosed with CFS.

I’m an IT guy by trade, so I was really surprised when I read their paper, completely understood the “link” that had been made between XMRV and CFS, and knew that it had already been proven false… all thanks to the TWIV podcast! Your podcast has always been interesting, but I had never been able to directly use anything in it.

I just wanted you to know that TWIV is also enjoyed by those of us that are not in field. Keep up the great work!

Paul

Taylor Ridge, Illinois

John writes:

Dear Dr. Racaniello,

I enjoyed TWiV 171, especially your lively discussion on our study of virus production from single cells (Timm and Yin, Virology).

Your discussion touched on what might happen if cells were infected with single virus particles or how virus yields might depend on the cell cycle. In previous work* we infected single cells will single virus particles (using a GFP virus, that allowed us to detect and sort single infected cells before the start of virus release); we found that in most cases ‘high-yield’ or ‘low-yield’ growth phenotypes did not persist from one virus generation to the next, suggesting the variation in growth behavior does not reflect viral genetic variation. Our population-level measures of virus yields on synchronized cells suggested some of the growth variation could be linked to the cell cycle — on BHK cells VSV made on average about six-fold more virus during G2M compared to cells in early S phase.

If you are interested, I’d be happy to discuss further. The ASV meeting will be in Madison this summer. If you attend, I would be happy to meet you and introduce you to my co-workers.
Best wishes,

John Yin

Systems Biology, Theme Leader

Wisconsin Institute for Discovery

University of Wisconsin-Madison

http://discovery.wisc.edu/discovery

Professor

Department of Chemical and Biological Engineering

University of Wisconsin-Madison

Cedric writes:

Dear TWiV Crew,

I read this article in today’s Wall Street Journal which discusses the growing number of pediatricians refusing to work with families who will not have their children vaccinated. It seems to me that this is an appropriate response on the part of physicians who do not want their other patients contracting preventable diseases in the waiting room just because one family has chosen not to vaccinate their child.

I was reminded of the Australian story, where families lose their tax breaks when their children are not vaccinated. Because I cannot see that scheme working in the U.S., it seems that this would be one of the few effective means left to physicians who can no longer persuade their patients of the importance of vaccination.

http://online.wsj.com/article/SB10001424052970203315804577209230884246636.html

Thank you all for the many hours of work you put into this podcast. As an undergraduate biology student, I really appreciate the head start it gives me in many of my science classes.

James writes:

Dear Prof. Racaniello,

I have been enjoying TWIV, TWIP & TWIM for some time. I am on faculty at a smaller institution and these podcasts have become my “journal club”. I have also begun to share the information and, in some cases, the podcasts themselves with my students – asking them to listen to the podcasts and then discuss what they’ve learned.

This past weekend, a thought occurred to me that, as a virologist, you might be able to provide some practical information for me. When I joined the faculty, I inherited glassware and other supplies. Among them were these pipettes. I’ve attached a couple of photographs of one (image one, image two). They are all 10 ml pipettes with a smooth plastic or Teflon tip. To me, it looks like they were designed to have removable/disposable tips. Since the lab I inherited had been previously used by someone with a virology background, I thought perhaps these were for tissue culture – something that transitioned between glass pipettes and disposable plastic pipettes. Have you or your colleagues ever seen/used pipettes such as these? I don’t suppose tips are still made for them, but I’m curious as to their history.

Sincerely,

James Masuoka, Ph.D.

Assistant Professor

Department of Biology

Midwestern State University

TWiV 177

John writes:

Dear TWIVvers,

In TWIV 173, you talked about a study on antibody levels to bird flu (H5N1) in various populations, and related this to infections that don’t cause serious enough illness to send someone to the hospital, or perhaps to get them tested for H5N1. I was curious whether some of the people with antibody to bird flu might have been exposed to the virus, but not ever infected. It seems like people who worked with poultry could be exposed to enough virus particles that even if they don’t replicate in the human body, they might still develop antibodies to them. Is this plausible? Since this is a gastrointestinal virus in birds, would droppings from infected birds be the main source of virus particles someone might be exposed to? If this explains some of the antibody against bird flu in the population, it should affect the estimate of how lethal the virus is when it does manage to infect a person.

A related question is: if we are worried about a potential H5N1 pandemic, would it make sense to add a related strain to our yearly flu virus, so that if it did start to spread, there would at least be some level of cross-reactive antibodies in people who’d been vaccinated?

Thanks again for your wonderful podcast,

–John

Lawrence writes:

I just wanted to express my appreciation for your podcast, and to tell you that I find your discussions fascinating. I am trained in engineering, but have a wide range of interests in all things scientific and am now turning my attention towards microbiology. Listening to your discussions of scientific publications and hearing the scientific mindset at work is soothing balm to my psyche in our world awash with banality, scientific illiteracy and anti-science. I keep a notepad with me as I listen and jot down words with which I am unfamiliar, and spend time afterwards researching their definitions which opens up new horizons and broadens my perspective in areas that I likely would never have encountered were it not for your podcasts. Thank you all very much for your time and effort.

Ebrahim writes:

Dear Dr. Palese, Dear Dr. Racaniello

I am a young student working on viruses in Heidelberg university, I am interested in Influenza and in viruses in general. I was watching the recent academy of sciences meeting in New York, and I just wanted to thank you so much for the position you took in the meeting, and I just could not convince myself against the idea that the real reason behind camping against the publications is anything but scientific, it might be political or whatever reason but I feel it is not based on scientific basis, since from my small experience in virology at least there are lots of experiments that might be far more dangerous than what have been done, and it might be helpful for me if you could give me your thought about that – of course if you have time for that.

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