Brachymeria Classification Essay

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:

I read your blog and look forward to all new posts. I was wondering if you were going to cover the news story on poultry vaccine strains deadly recombinant?

If so I would appreciate if you could address the following questions in your blog, as none of the articles so far seems to be covering this issue.

Question 1: how many genomes of viruses carried by people who have died or have suffered long-term effects following vaccinations have been fully sequenced?

Question 2: following on above (assuming the numerical answer is low/close to zero) how can we rule out with absolute certainty the possibility that some of the severe or prolonged negative reactions to vaccines are NOT due to recombinant or mutant viral strains (including possibility of vaccine+wild strain recombinants)? Are there any large scale study in the pipeline meant to address this question?

Larissa writes:

Dear TWiV Panel,

I have been looking for a list of papers reviewed by the three podcasts recently and I can’t seem to find one. Is there a list on your website of papers reviewed or should I just listen to TWiV(P)(M) with a pen and paper at hand always?

Thanks for all the great dissemination of scientific literature, it helps fill what would otherwise be many unscientific hours.

Warm Regards,

Larissa

Oren writes:

Dear lords of the Twiv.

It is a pleasure writing to you after being a long time fan (the weather in Tel Aviv is extremely hot and humid from April to October).

The show is great and keep me up to date in aspects of virology not in my direct field.

Well, I probably got the Twiv bump (Twiv 115 – color me infected) as now I am starting my own lab in the medical school at Tel Aviv University.

We are currently trying to upgrade the virology lab for the medical students and make it more appealing.

We have low budget wet lab that complement the medical students virology course.

If you or your listeners have any idea for an interesting way to attract medical students it will be highly appreciated.

Keep on the good work and Thank you,

Oren

Dr. Oren Kobiler

Clinical Microbiology and Immunology

Sackler School of Medicine

Tel Aviv University

Marcin writes:

Hello Viro-cides!

Can you please provide your comments to the attached editorial? It seems rather depressing that there are investigators out there that believe that if scientists don’t work 24/7 then they are not doing a good job. It seems that it is especially true at Johns Hopkins (see another recent article at: http://www.nature.com/news/2011/110831/full/477020a.html).

Thanks a lot, and keep up the good work with the delightful and engagin podcast! I just suggested to my summer mentee to listen to you and I believe he’ll get virally “hooked” as well!

Best,

Marcin

Clarissa writes:

Hi Vince and Rich,

great discussion!

Just to explain why we grow Cotia virus at 34oC. It grows better when we infect cells at 50% confluence. Actually, if we started plaque assay with 80% confluence at 37oC as we usually do for vaccinia, we’d get no plaques at all after 11 days of infection. Monolayers must be infected at 50% confluence or even less than that, and we set the growing temperature to 33oC-34oC in order to keep cells growing slowly. So I believe the virus grows better under these conditions not because of the temperature, but because it doesn’t like old, confluent cells. The adjustments in growing conditions in order to plaque purify Cotia virus took us over 6 months of work…

And yes, I agree with you that this paper has a lot of classical virology. I’m glad we stuck with this despite the opinion of most referees to remove these data and just leave the genomic stuff and phylogenetic analysis! And I’m glad that there are still several virologists who appreciate this kind of assays and pass this to their students.

Gopal writes:

Dear TWiV-ers

Since TWiV has, from time to time, gone beyond virology to discuss how science ought (or ought not) to be done, I thought I would bring this article that appeared in TheScientist to your notice.

http://the-scientist.com/2012/07/01/alls-not-fair-in-science-and-publishing/

Regards,

Gopal N. Raj

Science Correspondent, The Hindu newspaper.

Kerala state, India.

Luis writes:

Dear TWiVessors,

A few months ago, I read in Nature a few notes by Prof. Robin Weiss about recent books on AIDS. One of them, “The origins of AIDS” by Dr. Jacques Pepin, attracted my curiosity and decided to read it. I have just finished it and I must say that it has been an excellent read. The author who worked in Africa many years, describes the likely events that probably started around 1920s with the transmission of HIV from a chimpanzee to a human and ended up in a world-wide pandemic.

In the middle, many societal changes: from the colonial rule in central Africa, establishing new cities in the banks of the river Congo; with mostly male migrants and a thriving sex market. Then, a surge in the use medical injections with non-sterile syringes to treat different diseases (trypanosomiasis, yaws, syphilis, malaria), and also political instability after the independence of different countries that weaken their medical systems and produce a dramatic loss of doctors and health professionals, apart from teachers, engineers, etc… Highly-qualified workers were brought from other countries, and in this context, the infection was exported to Haiti and beyond. Furthermore, uncontrol blood trade in the 70s may have contributed to amplify the infection.

The book is a wonderful combination of contemporary history and epidemiology and health science.

The link for the commentary on Nature is:

http://www.nature.com/nature/journal/v482/n7386/full/482468a.html?WT.ec_id=NATURE-20120223

For the book:

http://astore.amazon.com/virologyws-20/detail/0521186374

Thank you very much again for your wonderful podcast and 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

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.

What is a Classification Essay?

In a classification essay, a writer organizes, or sorts, things into categories.

Three Steps to Effective Classification:

  1. Sort things into useful categories.
  2. Make sure all the categories follow a single organizing principle.
  3. Give examples that fit into each category.

Finding Categories

This is a key step in writing a classification essay. To classify, or sort, things in a logical way, find the categories to put them into. For example, say you need to sort the stack of papers on your desk. Before you would put them in random piles, you would decide what useful categories might be: papers that can be thrown away; papers that need immediate action; papers to read; papers to pass on to other coworkers; or papers to file.

Thesis Statement of a Classification Essay

The thesis statement usually includes the topic and how it is classified. Sometimes the categories are named.

(topic)...(how classified)...(category) (category) (category)

Ex: Tourists in Hawaii can enjoy three water sports: snorkeling, surfing, and sailing.

How to Write an Effective Classification Essay

  1. Determine the categories. Be thorough; don't leave out a critical category. For example, if you say water sports of Hawaii include snorkeling and sailing, but leave out surfing, your essay would be incomplete because surfing is Hawaii's most famous water sport. On the other hand, don't include too many categories, which will blur your classification. For example, if your topic is sports shoes, and your organizing principle is activity, you wouldn't include high heels with running and bowling shoes.
  2. Classify by a single principle. Once you have categories, make sure that they fit into the same organizing principle. The organizing principle is how you sort the groups. Do not allow a different principle to pop up unexpectedly. For example, if your unifying principle is "tourist-oriented" water sports, don't use another unifying principle, such as "native water sports," which would have different categories: pearl diving, outrigger, or canoe racing.
  3. Support equally each category with examples. In general, you should write the same quantity, i.e., give the same number of examples, for each category. The most important category, usually reserved for last, might require more elaboration.

Common Classification Transitions

  • The first kind, the second kind, the third kind
  • The first type, the second type, the third type
  • The first group, the second group, the third group

Remember: In a classification essay, the writer organizes, or sorts, things into categories. There are three steps to remember when writing an effective classification essay: organize things into useful categories, use a single organizing principle, and give examples of things that fit into each category.

Below are some sample classification essay topics:

  • Classification of historical events in US
  • Countries classification (territory, popularity, etc)
  • Sport Cars Classification
  • Most Popular TV Shows in America
  • Classification of Physiological Diseases

You can choose essay topic for your classification essay you are familiar with.

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