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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.
Richard W. Compans
Professor of Microbiology and Immunology
Emory University, School of Medicine
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:
Love the show.
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,
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.
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.
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").
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.
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.
sent by Lance via Twitter:
Matt Frieman writes:
A handy temperature chart for TWIV
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.
Ricardo Magalhaes, Ph.D.
Associate Professor of Microbiology
Faculty of Health Sciences of Fernando Pessoa University
(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
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 :)
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.
Houston rabies case poses new questions about age-old illness
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
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).
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.
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.
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?
lay-reader in Goodrich, TX
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!
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!
Centro de Biologia Molecular Severo Ochoa (CSIC-UAM)
Just in case you haven't seen this. Sort of timely, after your immunology podcast. Perhaps your son, the game player, can evaluate?
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.
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.
"...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?
"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?
"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.
"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.
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 :P 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:
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.
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,
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.