Sam writes:
Hi TWIV Team,
I just listened to TWIV 433 and while I was very interested to learn about anti-viral mechanisms in my favorite nematode worm, I have to make a few points. C. elegans is a species of self-fertilizing hermaphrodites with a very low incidence of males. While there are some male-female Caenorhabditis species (such as C. afra), this is not the case with C. elegans. N2 is standard wild-type strain of C. elegans first isolated by Sydney Brenner. Nematode growth medium (NGM) is essentially a non-selective solid bacterial medium which is generally seeded with the E. coli strain OP50, which the worms eat. The worms cannot eat the NGM itself and once the bacterial lawn is eaten, will starve (they will adopt the dauer stage and can survive without food in this way for many months).
I’m a big fan of show. Keep up the excellent work.
Sam in Toronto, Ontario.
Steve writes:
Hi Vincent et al,
Interesting programme this week.
I love all the carefully thought up entomological and morphologically descriptive words–they are so much better than the alphabet soup being used to describe biochemical entities!–: good descriptive names for the various parts and life stages enable different species to be compared, so that you can see how evolution acts on each segment of, say ‘the fundamental segmented worm’, to gradually develop the increasing complexity of all the vast variety of arthropods. A good name for each structural component of the basic ‘bug construction kit’ makes it possible to describe very complex features with great accuracy, on a ‘bug blueprint’, so that readers know exactly where to look to see what you want to draw attention to.
I’m not an entomologist, and I’ve not read the paper, but, when I hear you wondering if ‘secondary sexual features’ is a mistake, I can imagine, that, if you are dealing with something that affects the development of an insect into functional or sterile males and females, you might want to distinguish between the functional females, and the phenotypical females that cannot reproduce (as in the case of honey bees, for example). Your authors probably mean to make sure that they can determine the effective sex ratio, separately from the outward sex ratio suggested by the visible phenotype, following each phase of the experimentation. That would be my guess if it isn’t a mistranslation.
If you want to see some more brilliant words, you might like to check out the Wiki on screwworm flies, which you could then cover in TWiP, as the outbreak in Florida has just been brought under control by successive release of sterile males–which works in this species because the females only have one breeding cycle. I’m sure that Dickson would relish describing the gory details of the infestation by the live-flesh-eating ‘primary screwworm’, as compared with the dead-flesh specialising ‘secondary’ screwworm–which is also useful in estimating time of death in found corpses, and even cause of death, where poisons are found in the insects’ guts.
http://wwww.promedmail.org/post/4923534
https://en.m.wikipedia.org/wiki/Cochliomyia
_______
Knowing Kathy’s love of Lego, and, now hearing that she says she has never seen ‘Alien’, you might like to get her interested in the idea, by showing her this famous scene from the movie:
https://m.youtube.com/watch?v=ZRfNqvJ264I
And here compared, blow by blow, with the original:
https://m.youtube.com/watch?v=DU-5XEdPgYU
Love that they even included the cat. 🙂
All the best,
Steve
Luton
Bedfordshire
England
Where Spring is sprung, the clocks have just gone forward, and wild plum blossom is ablaze in my overgrown garden.
Jimholy (Jim-Hoe-Lee) writes:
Dear Vincent et. al
I thoroughly enjoyed your discussion on parasitoids, everyone was friendly and made the discussion fun. At the time of this writing it is a dreary 40֯ F, there is still snow everywhere. I’d like a chance to win that book. You guys are the first science podcast I have ever listened to, as a millennial I normally consume my science via YouTube videos (most notably scishow). I am a senior Molecular Biology major at Skidmore College taking Dr. Hilleren’s Virology, RNA and Biology of Cancer classes, so there is a fair amount overlap between the classes.
In China, they have already begun genetically engineering 3n human embryos to cure lung defects. https://link.springer.com/article/10.1007%2Fs13238-015-0153-5. What are your thoughts on genetically the engineering the viruses to skew the sex ratio in the other direction as a way form of improving pest control? There is a C2c2 CRISPR derived system that can edit targeted mRNAs. http://science.sciencemag.org/content/early/2016/06/01/science.aaf5573
Sincerely,
Jimholy (Jim-Hoe-Lee)
P.S In traditional Chinese symbolism the Yin-yang each swatch contains the seed of its opposite, I thought it was a clever play on symbolism where you would have the seed of male skewing viruses inside of the females (not sure how intended that was). In standard Mandarin Pronunciation Song is pronounced (Soong), and zhe (zh-ugh) (like you’re soft grunting), he (h-ugh). I really appreciate that you guys trying to get the pronunciations correctly.
Eric Delwart writes:
Dear Vincent and Twivome
This study shows how human genomic data can be repurposed or mined to analyze a part of the human virome. To put the scale of the analysis in context: The 1 petabyte amount of data used here is the equivalent of 100 thousand runs of the smaller MiSeq Illumina machine typically used for viral genomes. The amount of data restricted the analysis to finding viruses using nucleotide sequence similarity only, rather than the computationally much more demanding translated protein similarity searches needed to detect divergent (ie “new”) viruses. The focus was on a small fraction of that starting data (~0.000005) that matched viral sequences.
As most of the people sampled were likely healthy, the viruses detected, with a few exceptions, are typical commensal blood borne viruses. The focus on blood cells left out the large majority of human viruses that are usually restricted to respiratory, skin, or enteric tissues. Because of the way human genomes are sequenced the viruses detected were largely limited to those that are associated with blood cells and have double stranded DNA genomes or at least form a dsDNA during their replication cycle. The dominance of the Herpesviridae reflects the focus on cellular DNA rather than plasma where these viruses are more rarely detected. Anellovirus were also commonly detected despite their single stranded circular DNA genome likely because they were caught in the act of replicating as rolling circle dsDNA intermediates. As expected the very common blood borne RNA pegiviruses (in Flaviviridae family) were not detected.
As you often state in TWIV finding viral genomes does not prove that the virus is infectious. Sequences from viruses known to replicate in bacteria, algae, amoeba, or fungi were also detected likely reflecting DNA contamination in the many reagents used to generate human genome libraries. Human tropism for these viruses has not been shown. Papillomaviruses and polyomaviruses sequences where also detected despite their known tropism being restricted to epithelial cells. Their detection in blood may reflect either other sites of replication or sample contamination with skin cells during phlebotomy.
So despite the bias of the starting material (blood cells), focus on dsDNA, and lower sensitivity relative to targeted PCR studies, the study shows that analysis of raw human genomic data can reproduce the known epidemiology for some viruses like the higher prevalence of HTLV proviruses in people of African ancestry. If similarly analyzed the growing amount raw human genomic data will allow large scale epidemiology for blood cell associated dsDNA viruses. Data from the major human populations located in either their ancestral or new homes may facilitate studies of the relative roles on these infections of human genetics versus geography and lifestyle. By combining the human genomic and viral information the identification of human genome polymorphisms associated with particular infections or high viral loads will also become possible.
Lots of these analysis will depend on available computing power. Maybe Facebook, Google or Amazon will have some to spare?
Andrea writes:
Suggestion, perhaps you could pick a random email out of the emails that you receive in a specific amount of time, say two weeks for example, this way people that listen to the podcast early and send in an email have the same chances as those that listen later.
I am assuming, of course, that you want to get the contest over as early as possible so that you can continue to clean out your office of all the extra books.
Seattle
Ken writes:
Vincent & Crew-
When I heard you were giving away books, I assumed they’d be gone long before I could type your address on my email. If you have not yet, please consider this submission.
I have been listening for a little over a year, since my friend Lauriel introduced me while we were talking about her research on AAV. She met you in Portland, and I remember hearing about your trip on TWIV.
I was also pleased to hear you read her email detailing the capsid proteins, on which her thesis was written.
I am a software engineer, and my knowledge of viruses is very limited, but I am a huge fan of science, and learn as much as I can find the time for. That is why I love listening to TWIV. I have to pause often and look up terms and papers– it keeps me on my toes. Keep up the good work!
P.S. It is cloudy, windy, and about 10°C here in Portland today, with a lot of rain in the forecast.
Ken
Alexandra writes:
The emerging infections book is still up for grabs! I just got into the wonderful world of viruses three months ago & you have definitely infected me with great fascination.
—
Alexandra Ortiz Rosa, M.Sc.
Virology Laboratory Research Assistant
Department of Microbiology & Medical Zoology
University of Puerto Rico – Medical Sciences Campus
Donna writes:
Dear TWiV crew
I heard on TWIV 428 that you had not yet received email #27 for the Emerging Infections book – would be great to add this to my collection. Even if I’m not the winner, I want to thank you for the TWiV podcasts
I’ve been listening since the Joan Steitz interview. My graduate work was in virology (VSV inhibition of splicing in Jack Keene’s lab in the 1980s). I meandered into other topics for postdoc and beyond. I am a lecturer at RPI (non-tenure track: 10+ years) where I teach a variety of molecular biology-related courses. I was excited when Virology was added to my teaching duties in 2015; this led me to your podcast via ViralZone.
I especially enjoyed your discussion of VSV UV inactivation as that was a technique I used extensively in my graduate work.
Thanks so much for your podcasts
donna
Donna E. Crone, PhD
Lecturer
Rensselaer Polytechnic Institute
Dept of Biological Sciences
Neil writes:
“Sparrow Urgent Care Physician Dr. Song Yu says although it feels similar to the flu, it’s actually a virus.”
Some other good quotes from this MD in the article: http://wlns.com/2017/02/19/viral-infection-going-around-mid-michigan-how-you-can-protect-yourself/
Maybe Kathy can try to do some in-state education…
Wow.
PS to add to the other podcasts list: Freakonomics. Especially my listener pick, 3 episodes called “Bad Medicine”…
http://freakonomics.com/podcast/bad-medicine-part-1-story-98-6/
http://freakonomics.com/podcast/bad-medicine-part-2-drug-trials-and-tribulations/
http://freakonomics.com/podcast/bad-medicine-part-3-death-diagnosis/
———————————————————–
Neil Parkin, Ph.D.
Data First Consulting, Inc
Belmont, CA
Sidd writes:
Hi TWIV team!
It’s 6C in Saint Louis, and I’d love to get a copy of the Emerging Infectious Diseases book!
I’m a PhD candidate at WashU studying RNA phages and viral dark matter. I’ve been listening to your podcast for about 8 years now (primarily TWIV and TWIM) and I think it’s great!
Thanks!
Sidd