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Letters

TWiV 201 Letters

Dennis writes:

Dear Vincent,

I am glad you had a chance to get a glimpse of the BSL4 world. You might remember that I have been trying for 1 1/2 years to get you to see the Galveston National Laboratory, a facility with an actual ACTIVE program and a number of very experienced PIs that currently work in the BSL4.

I wish we would have had the chance first especially for TWIV 200.

A very disappointed,

Dennis

Jim writes:

Gents,

A recent BBC Health Check program included a segment about rabies which notes that vaccines derived from dog rabies may only be effective for people bitten by a rabid dog, but not a bat! I've attached the program and it's the first segment which is only about four minutes long. A Dr Behrens (link to some of his advice) from the London School of Tropical Medicine and Hygiene is the speaker and source of the comment. Are there multiple vaccines for rabies? This complicates things....

Regards,

Jim

Smithfield, VA

Mattias Schnell responds:

All USA bat rabies is covered by the current rabies vaccine but its different for bat derived rabies in other regions.

Two thing are important to know:

1) When people talk about rabies they normally mean classical rabies virus (RABV) and this is still the most important member of the genus Lyssavirus. Almost all death of humans is caused by RABV transmitted by dogs.

Big problem in developing countries (South America, India, Africa, China, Asia in general). In Europe and USA we do have rarely rabies transmitted by domestic animals because we do vaccinate that problem is gone.

We still have a large rabies problems in wild animals (skunks, raccoons, foxes) but if somebody get bitten by a rabid animals we do postexposure treatment, which is 100% efficient if applied correctly. About 30,000 people do receive postexposure treatment in the USA every year (that is not cheap). We do have about 3 cases of rabies in the US every year but they were imported (people who traveled an got infected) or they got infected by bats. This brings us to the bat topic. All bat derived rabies virus in the USA is classical RABV so postexposure will work. However, people might not realize that the have been bitten by bats (small teeth). So the problem in the US is more that people do not realize they were exposed or do not know that bats are transmitting rabies virus.

2) Bats are very likely the natural host of lyssaviruses. Bats seem not to be as sensitive to rabies virus and a lot have actually antibodies. That doesn't mean they dont get rabies it but it is probably not 100% lethal. Make sense if you think how close they live together. Also important, there are bat derived lyssaviruses, which are antigenetically different from RABV so the vaccine doesn't protect. This is the case for the to African lyssaviruses mokola and Lagos bat. So for these viruses there is no vaccine even it would be easy to make one.

Hope that help - a bit more info is in the powerpoint file. As usual things are simplified and not everybody probably would agree with me....

All the best

Matthias

Matthias J. Schnell, Ph.D.

Professor Department of Microbiology and Immunology

Director Jefferson Vaccine Center

Jefferson Medical College

Peter writes:

Hi Twiv crew,

The Texas Wild Child was mentioned on 192 (listening now). Did you see the August Wired?

http://www.wired.com/wiredscience/2012/07/ff_rabies/

The article describes a therapy for rabies victims and its controversy. How did I miss this? 6 survivors (of 41 attempts) since 2004? Not including the Wild Child.

I would love to hear your thoughts, especially since this was an article I could easily follow, not a research paper.

Thanks for all you do!

Peter

Micki writes:

Hi guys,

Interesting short article on Fox News about Vampire bat bites conferring resistance to Rabies. What are your thoughts on the subject?

http://www.foxnews.com/scitech/2012/08/04/vampire-bat-bites-help-shield-from-rabies/

Great show - thanks for all your hard work. - Micki / Simon Lab / UMD

PS - have you thought about doing a show about Rhabdovirus that would include a plant rhabdovirus scientist? Maybe Andy Jackson or Michael Goodin. Just a thought . . . . . . .

John writes:

Rabies seems to be in the news these days. There is also a new cultural history of Rabies, entitled "Rabid" by Bill Wasik and Monica Murphy. I'm listening to it on audible and it's fascinating. Regards, John

http://www.nytimes.com/2012/08/07/health/study-suggests-that-rabies-may-not-always-be-fatal.html?emc=eta1

Cristiano writes:

Dear TWIV hosts,

I caved in when my 4 y.o. daughter asked me for an iTouch last year. I resisted for as long as father could. But, in the end, I gave up and bought her one.

Few months later, she cracked the screen, lost interest in it and asked me for an ipad, instead. Initially I laughed at her request, but, since I caught her mother looking for an iPad ad in the weeks preceding mother's day...guess what? Yes, you're right, I caved in again and bought them both the latest generation iPad.

I noticed there was nothing wrong with the iTouch, except for the cracked screen. So, I decided to fix it myself. A few attempts later and the broken iPod was good as new. "What am I going to do with this?" I thought, realizing that the whole world was ahead of me with regards to popular electronic gadgetry.

"Play games", said my daughter.

"Listen to podcasts", suggested my creative wife.

"How do you do that?", I asked.

That question has thrown me to an entire new world. From then on, it was just a matter of hours until I found your program. [ks: don’t read next line?! ad: Definitely read the next line, then act regretful when you get to the parenthetical part.] And I truly fell in love with it (please, please, please, don't say that out loud on the program! I've got a reputation to maintain!)

I'm a virologist as well. I started studying baculoviruses when I was an undergrad back in Brazil and eventually got a BSc degree from the University of Brasilia. Soon after, I went to Japan to study more about "baculos" and pursue my postgrad degrees (MSc and PhD) at Nagoya University. In 2003, once I could safely display the "mission accomplished" banner, I sailed away to the uncharted waters of New Zealand for a short postdoc position at the University of Otago in Dunedin. A place I now call home.

After my post-doc experience, I became interested in the field of Science Communication and documentary filmmaking and was fortunate enough to have stumbled across a a postgrad course at the University of Otago, which combined these two topics. For my final project, I decided to combine my virus research expertise and tell the story of the Auckland Island Pigs. Here's a link to the movie:

http://vimeo.com/20099254

The movie, posted by co-director Adam Thompson, talks about the pigs being commercially exploited as promising xenotransplantation tools for the treatment of type 1 diabetes. Long story short, a couple of hundred years of complete isolation " made" the pigs germ-free. At least, that's what the charismatic mayor of the city where the pigs are now kept and the biotech company tells us all. But the truth is far from it. The pigs have very low copies of PERVs (porcine endogenous retroviruses) integrated in the pigs genetic make-up

http://www.ncbi.nlm.nih.gov/pubmed/21545811

I would like to invite you, dear TWIV hosts, to watch the short movie (for some feedback) and perhaps discuss about PERVs in the future. In addition, I would love to know your thoughts regarding xenotransplantion and viruses, in general. That would mean the world to me, as, even after having finished this movie, I still can't reach a verdict. Do we abandon this live-saving technology due to its potential risks of pandemic proportions or embrace it and utilise it in large-scale xenotransplantations world-wide?

Please keep up with the outstanding work you guys are doing with the program. Your ideas and comments are truly inspirational!

PS: Really sorry about the animations in the pig movie. We received no money for this project and had to be creative with explanatory animations.

PPS: http://www.youtube.com/watch?v=ChIeTB-XHsM is another movie I made. It only touches the issue of varroa-mites as carriers of honeybee viruses.

Cris Felipe-Alves, PhD

Post-Doctoral Fellow

Virus Research Unit

Microbiology & Immunology Dept

University of Otago

Matt Evans writes:

Hi Vince and gang,

Last week you had a letter from an Olympic athlete who wanted to know how he could stay in touch with science while training. I was amused when Rich said there is no way you could work for your phd and train for the Olympics at the same time because that is exactly what my student, Maria Michta, just did. She was the only female race walker from the US to compete in London. Now she is back in lab as a full time student. Training was balanced carefully with lab work over the last few years, but being right next to Central Park made it a lot easier. She even had a first author paper while training.

Not bad huh!

Matt

KH writes:

Dear TWIV,

I’m doing an EPQ (independent research qualification taken at end of high school) on the eradication of polio, and whether the current attempt is worthwhile or not. I have a vague memory of it being mentioned in TWIV that it is advantageous for attenuated poliovirus to regain virulence, but haven’t been able to find anything on this anywhere. Could you give me any further information, or direct me to where I can find it?

Regards,

Katherine

P.S. TWIV is fantastic; it was what inspired me to choose a virology based topic for my EPQ and to apply for university courses which include virology - prior to listening I had very little interest in it.

Sydney writes:

Good afternoon! I know you're busy, but I hope this email finds its way to you. I've been listening to your podcasts for quite some time now. I really admire your innovation and ingenuity in regards to educating the general public about viruses.

I've been interested in virology and host-pathogen interactions for quite some time, especially those of newly emerging viruses. This led me to pursue my MS in Entomology last fall. I have one year to go, and I'm beginning to look at PhD programs in virology in order to combine the two skill sets. Viruses like Ebola, Hendra, and Nipah are especially intriguing to me, and I'd really love to work with newly emerging pathogens. However, as I search for PhD programs, I'm finding that the number of researchers working in this area is low. It seems that the majority of this work goes on in level 4 laboratories (of course) by researchers, rather than professors. I was curious to know if you could recommend any programs to me that might be a good fit, or, if you could tell me whether working with another virus for my PhD would affect my ability to land a job with level 4 agents later in my career.

Any advice would be great! Although I've almost completed my Master's degree, I still feel like a nascent scientist with a lot to learn. You, Rich, and Alan help tremendously though!

Have a great day, and I look forward to hearing from you.

Sydney

Dallas writes:

Twivers,

Still going through old podcasts and still don't understand virus, but I do know a little physics.

On using the supercritical CO2 to create a dry virus may allow viable virus particles to survive. The killing of enveloped virus on drying may have to do with the surface tension of water changing the physical structure of the virus particle and drying under supercritical conditions the surface tension of the gas/liquid interface goes to zero.

See: http://en.wikipedia.org/wiki/Aerogel

To see how an open gel type structure can be dried without destruction -- just a common example that shows the principles. If the virus didn't change upon drying, it is small enough that the time it would take to rehydrate from the gas phase at 100% RH at lung temperatures and lightly hydrophilic surfaces could be so fast that no structural collapse would occur on rehydration.

Someone else probably already answered this physics type question.

Dallas

Scientific Hatcheries

http://web.mac.com/deweaver/bottom_trawling/Welcome.html

Nathan writes:

It was mentioned in TWiV 178 that Puerto Rico doesn’t currently have other mosquito-borne viruses like yellow fever or malaria. Can this be attributed to anything other than luck? Do any countries undertake efforts to curtail the spread of viral vectors (by controlling used tire trade or otherwise)?

thanks,

nate

Nathaniel writes:

This question is in response to episode #182.

You three discussed the benefits of immunizing in the skin rather than the muscle. This may be a naïve question, but wouldn’t injecting vaccine directly into the blood stream be better than both skin and muscle? Is this an issue of medical “difficulty” and patient compliance?

Bronwyn writes:

Dearest TWiV hosts (reservoir?) I’ll try to be as brief as possible, though typing that rather than simply doing it is probably not helping there… ANYWAY my name is Bronwyn, I’m a 2nd yr biomed undergrad studying on Australia’s Sunshine Coast and though only newly infected, i’m immensely fond of your show! I love the break down/discussion of papers and new research which saves me drowning in the great sea of articles that is; scholar/pubmed/scidirect/etc/etc/etc. And as an undergrad wanting to get into research; #184 on the broken science system (and more importantly how to work towards fixing it + just survive in the meantime) was BRILLIANT, i clicked download on the Casadevall and Fang papers as soon as i had played it out, which meant that they had just finished by the time i finished playing it through the second time over. I’d been getting despondent over the dog-eat/poison/cripple/render-otherwise-harmless world that science research seemed to have manifest itself as, a model one would have expected from a somewhat business-like paradigm, not the province of a collaborative pursuit of understanding so that we, as a biologically social species, might go about interacting with the world in a more intelligent way. But enough ranting; essentially i love your work guys, and incidentally its about 20’C and a bit overcast here and there, which is really quite cold for us -winter just started.

But now to get to the reason why I’m spamming your already inundated inbox: earlier this term in a micro class my lecturer was talking about plant viruses and i couldn’t help noticing they, for the most part, have RNA genomes rather than DNA… i was curious and asked but she was unaware of any reason why and couldn’t find any explanation when she researched it a bit later, either could i… any ideas??? Is this possibly a quirk of nature arising from a/an RNA-containing evolutionary forbearer/s or does anyone know of there being some sort of selection preference for RNA genomes in plant viruses?

Also; I was watching a video: ‘MIT World’ talk on Global Pandemics (Nov 17 2009) given by Hidde Ploegh (Prof. Biol MIT) available from itunesU (or http://video.mit.edu/watch/global-pandemics-9508/), it’s a soap-box-talk-night-sort-of-thingy… ANYWAY Hidde briefly discusses the FDA-approved method of flu vaccines production, pointing out the fact that not all flu strains grow equally well in eggs, which limits the strains covered by an American-made vaccine to those that perform sufficiently in chicken eggs. Is this a serious limiting factor in the vaccine quality or merely something that needs to be kept in mind when making a vaccine? In Europe flu strains are grown in cell cultures, this would eradicate the problem of allergic reaction is caused by chicken proteins, is there any other reason why an allergic reaction would occur in response to a vaccine? and it’s 1hr 5 minutes long...; maybe HP part is 15 minutes long then there’s Q&A, according to the introduction][I listened to about 20 minutes of it, didn’t get to any juicy parts]

If you’ve time i recommend watching the talk, there’s a great dismissal of an ‘evil drug company flu vaccine hiding’ conspiracy theory and a criticism of the economic priorities of funds allocations in research and of the concern (paranoia?) the US seems to have over biodefense (despite the lack of reasonable threat assessments) @38:56 - 42:07. Just think; this was 3 years before the NSABB censored the Kawaoka and Fouchier research! But my favourite part (if it’s not the fact that he’s wearing bright red pants) is the final word he gives on the moral obligation of vaccination and the dangerous selfishness of people who rely on herd immunity; it’s a serious problem i think; -here in oz there is a massive anti-vaccination sentiment, rooted in a distrust of science/medicine/drug companies and fear of vaccination side-effects like autism from a measles vaccine (jeez looks like a symptom of the winner-takes-all-system with its pressure to publish giving rise to bad science and fraud - A retraction does not and cannot undo the damage done by bad science). This attitude seems to be concentrated in more alternative towns like Byron. Paul Corben (director of NSW North Coast Public Health) said there had been TWICE the level of disease in Byron Bay as had occurred in Ballina, a town pretty well adjacent to it (this info is taken from the ABC TV show Catalyst Episode 9 of 2012). Is regional social psychology also a big factor in American vaccination rates? Do public health systems attempt to address this? I mean wouldn’t unvaccinated people, when concentrated into small geographic areas be so much more dangerous than if they were dispersed as the statistics for the unvaccinated: vaccinated ratio make it appear??

I don’t expect this to be read on air or anything, I’d just really appreciate any answers/info/links/TWiV episode suggestions. i’m still working my way through the back catalogue (just finished 2008) in addition to listening to current episodes as they’re released so i do not doubt that some of this would be addressed therein. I’m especially curious in regards to the apparent plant preference for RNA…

oh dear… Short-message-fail: that was so much longer than the paragraph i had originally intended, well my apologies and many magnitudes of thanks from down under!

http://www.mailtribune.com/apps/pbcs.dll/article?AID=/20111228/NEWS/112280317

http://public.health.oregon.gov/preventionwellness/vaccinesimmunization/pages/research.aspx

T. Jack Morris responds:

I can think of no fundamental reason for this to be the case other than an accident of evolution. Here is the rationale. It turns out there are no true dsDNA viruses. There are pararetros like Cauliflower mosaic and ssDNA viruses like geminiviruses, so it is not because plant cells could not support true DNA virus replication. It is not likely a cell to cell movement restriction because there are plenty of viruses of papilloma size that infect plants. It could have something to do with the nature of plant meristems where cell division is primarily restricted. It is a question worth considering, perhaps at the TWIV. I am copying a colleague with whom I have had this discussion.

Jack

Dallas writes:

Just a quick comment on the podcast covering journal retractions and other "scientific" errors. A comment was made that the problems seems to be in the first rate journals which have the most retractions -- at least the ones we hear about. However, if you want to find a lot of papers that should be retracted, the second, and third tier journals have even more junk, advocacy science and false information, but most of it isn't worth anyones time to bother proving false or pointing out the errors.

To complicate the problem in the second and third tier journals, you have advocacy groups of various types (ranging from environmental groups to anti-global warming groups) playing a bootstrapping game to create scientific "facts" with great "truthiness" that can be cited in first tier journals. For an example of this bootstrapping, a friend of mine in academia was charged with the task of tracing the source of a scientific "fact" about damage from the aquaculture industry on the environment that found it way in proposed regulations and into law suits. It turns out that an activist group created a damage estimate out of a "consensus" feel among other activists and got it past the reviewers in a third rate journal, after adding a lot of caveats about this estimate just being a SWAG (scientific wild ass guess) with no data. The activist group then got another publication in a similar area in a second rate journal referencing the first article, without the caveats, which was then referenced in a first rate journal by a related activist group with a common funding source. Being in a first rate journal, it was now a proven scientific "fact" and used by regulators being lobbied by the activists groups. The industry was then facing a scientific "fact" with great truthiness, which didn't match with their unpublished observations.

With the high frequency of manure in the second and third rate journals, it may be a good training exercise for starting graduate students to plow through some of these journals and pick a paper to reproduce the most suspicious parts or demonstrate error in their methods or analysis. They would end up learning a lot about everything from good lab work to ways of analyzing the data. It may be a good way to sharpen the thinking of grad students and reinforce the message that all you read is not true. It would also force the students to go through a lot of articles looking for particularly bad one for their class project and read them all very critically. A year later, when they are writing a paper, have them visualize how their class mates would cut it apart and you may get better first drafts.

If you want, I could provide several examples from the environmental literature, especially aquaculture, where truthiness rather than true "facts" dominate the literature.

I am a semi-retired retreaded physic/thermodynamics/engineering type who spent 3 decades solving environments and aquaculture problems (heavy into using microbiology to destroy hazardous materials or convert waste products -- it is all about the bugs and bug habitat), who is slowly working my way through old twig podcasts with great delight. Keep up the excellent work educating senior citizens about the fascinating world of virology. I have a great interest and little knowledge about phages in the real world, where they seem to often be the "keystone" species -- not the lions and sharks discussed in ecology classes.

Thank you,

Dallas

PS: In case you don't know, various shrimp virus do a billion+ dollars damage to the world wide farmed shrimp industry every year (90% of the shrimp we eat in the US are farmed). Don Lightner mailto: This email address is being protected from spambots. You need JavaScript enabled to view it. at U of Arizona is the top man in the world on shrimp virus and may be an excellent guest. The shrimp industry is far more sophisticated about identification, control, biosecurity and managing virus than any other industry I know about. PCR testing at the farm level. I have been in shrimp hatcheries in the middle of remote areas of Central America that make the our top rated local US hospitals look like cesspools of bacterial and viral contamination in comparison -- very tight biosecurity.

Dallas, Ph.D.

Scientific Hatcheries

Huntington Beach, CA

http://web.mac.com/deweaver/bottom_trawling/Welcome.html

Neva writes:

Howdy TWIVs,

This article in Ars Technica on disrupting the publishing model of papers in biological science might interest you and your fans.

http://arstechnica.com/science/2012/06/new-open-access-journal-aims-to-disrupt-scholarly-publishing/

Keep up your valuable and entertainlng podcasts!

Neva in Buda

Josh writes:

Dear TWiV Doctors,

You will probably get a thousand emails about this, but there was an article in Nature about curing Ebola virus in monkeys. Here's the link:

http://www.nature.com/news/antibody-cocktail-cures-monkeys-of-ebola-1.10821

Sarah writes:

Hello Twiv-ologists,

The June issue of ASM's Microbe magazine had a feature article on virus-induced obesity that had so many holes I had to break out my pen and write all over it. I followed the references to the 2005 paper that the article seemed to be based on, and as much as I believe in the possibility of an infectious factor in obesity, my BS meter just kept going off here. Looking past the incredible number of variables that weren't even considered in data collection, questionable sample handling, missing context, and leaps in logic, I couldn't get past two fundamental issues. One is the author's apparent belief in a causal connection between the initial detection of this virus in 1978 and an epidemic of obesity that seemed to begin around the same time (detection and emergence of a virus are two quite different things). The other is the glaring conflict of interest evident in his founding of a company that makes assays to detect this virus for consumers. The company's website skips scientific caution and flat out states that Ad-36 causes obesity. (The author is also the editor of the journal in which the 2005 paper was published... how awkward is that for peer reviewers?)

I'm coming off of three recent influences on the importance of keeping a skeptical mindset and using critical thinking as a verb -- the dogged insistence of Mike Osterholm's statements during the NSABB brouhaha, reading The Panic Virus, and then reading A Demon Haunted World by Carl Sagan. It seems like freight trains of misinformed, truthy opinion can leave the station before anyone figures out what's happening, and by then all any rational person can do is stick to their evidence-based guns and let the situation run its course. (I'm not saying Osterholm is being truthy like Jenny McCarthy, but I've wondered whether he thinks that someone in the biowarfare labs in Iraq are just waiting to get their hands on Fouchier's paper.)

My husband teases me because I don't mind writing a letter about something on which I have an informed opinion, whether it's about a product, customer service, a news article, etc. He has a point; sometimes it's better to just let it go. There are limitations to all experiments. But when you all come across papers like this that make you just cringe, what do you do? Is it better to let it slide, write a critique, or just talk about it on TWiV? :-) As I move into a healthcare career I'm concerned about these issues not only for the sake of science but for the sake of public health policy, grant funding, and what new damage could be done with the combination of the media and outspoken narcissists or misanthropes. I now not only see microbes everywhere I go but also the subtext of human behavior. Gray hairs may be soon to follow (just kidding).

Thanks and keep having fun!

Daniel writes:

http://www.cnn.com/2012/06/18/world/asia/pakistan-taliban-polio/index.html

Judi writes:

Thought you might find this useful....

http://sciencereview.berkeley.edu/top-10-free-apps-for-scientists/

Wink writes:

I noticed that you sometimes do on-air internet searches and end up with commercial results. Switch to DuckDuckGo.com to regain your integrity. It is also more efficient. The URL "ddg.gg" gets you right there. Once you are ready to "Quack" for something, try "bang searching." Examples of bang searching would be "!amazon Racaniello" or "!cdc dengue".

Wink, MD

Infectious Diseases

Josh writes:

Hello TWiV Doctors,

My listener Pick of the Week suggestion is 3.091x: Introduction to Solid State Chemistry from MITx(edx). This is the online version of the MIT freshman class 3.091: Intro to Solid State Chemistry. It begins October 15th, 2012. It's free, there are no prerequisites, and if you successfully complete the course, you get a certificate of completion from MITx.

https://www.edx.org/courses/MITx/3.091x/2012_Fall/about

I realize this is not biochem, but I think it is still relevant for TWiV listeners. I took(and completed!) the first MITx online class, 6.002x: Circuits and Electronics, and I will tell you that they do not water down their classes just because they put them online. It was MIT hard, and it was a brutal process getting through it.

Some of us were saddened to learn that the excellent lecturer Dr. Donald Sadoway would not be the instructor. However, in a bonus for TWiV listeners, Dr. Michael Cima will be the instructor. It's a bonus for TWiV listeners because his speciality is more medical than Dr. Sadoway. Specifically in nano-technologies for medical monitoring and drug delivery. Here's a video where he runs down what his is working on:

http://ki.mit.edu/people/insidethelab/cima

In addition, edx is offering PH207x: Quantitative Methods in Clinical & Public Health Research, through the Harvard School of Public Health. 5 other courses are offered through a combination of MIT, Harvard and UC Berkeley. You can see all of them at edx.org.

Thanks,

Josh

 

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