Hi Vincent and Co. (there must be a better term for a group of virologists, a plaque of virologists perhaps?).
A couple of quick comments on TWiV 367:
First, great to hear Coyne Drummond again. If one of your ex-students is on TWiV, you must have “made it”. He has some really gorgeous data and seems to be doing very well in spite of my influence in his earlier career.
A second comment, that I am sure that Coyne would have corrected you on, if he had not had to go back to the lab last week. Prokaryotes refers to cellular organisms that are lacking nuclei, so includes both Bacteria and Archaea, not just Bacteria. Vincent is correct that Archaea have CRISPR/Cas systems, in fact more archaeal genomes have CRISPR/Cas systems than bacterial genomes. In Archaea CRISPR/Cas is almost universal, in Bacteria considerably less so. Why this is the case is mysterious, it may have something to do with more bacterial genomes having restriction endonucleases than archaeal ones do.
Norm Pace wrote an interesting essay about getting rid of the term “prokaryote” that is still available at his website: https://mcdb.colorado.edu/courses/4350/2010pdf/Pace.MicrobiolToday.2009.pdf. There has been some interesting discussion on the subject, see Tanya Noel’s nice more recent blog post about it: https://tanyacnoel.wordpress.com/2014/01/17/pervasive-persistent-problematic-prokaryote/
Keep up the great podcasts (and talking to my ex-students).
This thing about Microcephaly is so scary. And the difficulty to achieve an easy way to diagnose it is also a complication, since a big part of our population already has contact with Dengue. (cross reaction)
What do you think about it?
Hi TWiV team,
It would be useful to do a snippet that gives a bit more information on Zika virus and its mode of operation:
Dear sir or madam,
In case you’re interested:
All the best,
Paul L. Bollyky, MD, D.Phil
Division of Infectious Diseases
Department of Medicine
Stanford University Medical Center
I have been a long-time listener of TWIV and I was having a conversation with a colleague the other day about Vaccine derived polio. I seem to remember a recent (in the last few years) conversation you may have had about some cases of vaccine derived polio in the US. I tried to look up some literature on the pub meds and googles but came up short. Do I remember a conversation that never happened?
I wonder what standard the NYT used to determine that Ebola is “one of the most dangerous viruses known to man”?
# # #
How The Times Covered the Ebola Epidemic
OCT. 6, 2015
Imagine covering one of the most dangerous viruses known to man. Then imagine doing that in a protective suit, face mask, boots and multiple pairs of gloves. How do you take notes? How do you hold a camera? How can you even see what’s going on?
The Times had more than a dozen reporters, photographers and videographers inside the Ebola zone in West Africa over the course of the epidemic. Collectively, they spent well over a year’s worth of reporting and shooting time chronicling the outbreak inside the three West African countries most afflicted. They produced more than 50 front-page articles about the outbreak and its effect on the region. In all, The Times has published more than 400 stories about Ebola, from at least four continents. The coverage won the Pulitzer Prize for international reporting in 2015.
Here, two staff members reflect on their experiences covering the health crisis.
Dear Professor Racaniello,
I very much enjoyed this interview with Prof. Damania on TWiV 359 (A Blossom by any other name).
Prof. Joan Steitz (mentioned in this interview and on a previous TWiV) and Blossom Damania are an inspiration to women in science everywhere.
It would actually be very interesting if you could do a TWiV with women scientists like Professors Damania, Steitz etc. together in one episode to talk about their collective experiences as outstanding women in science.
It would be inspiring to young women scientists like me.
Please keep doing what you are doing with TWiV.
You have an enormous impact on budding scientists like me.
Thanks for all you do,
Greetings TWiV team from an unseasonably warm (16°C), if rather damp United Kingdom,
I have some general virology questions for you.
When virions exit host cells without killing the cell, either by budding or exocytosis, is there any specific mechanism that prevents the newly released virions from immediately attaching to the same cell?
Is is just a numbers game in that enough virions are released that it does not matter if some are wasted attaching to an already infected cell.
Does it take some time for the virion to mature to become infectious so that by the time it is infectious it is no longer in close proximity to the host cell?
Is there a mechanism that prevents virions attaching to a cell infected with the same virus?
I suspect that given viral diversity that all of the above could apply to different viruses.
I thought that you may like satire as a pick of the week:
This short video succinctly and graphically shows why the Measles virus so devastates the immune system. Also states that 122,000 people died of Measles in 2014. It might not change anti vax minds but can help those who have doubts about vaccinating.
Cold nights in Santa Cruz, in the thirties. Thankfully we’ve had three rainy waves but not yet prolonged storms that we need.
Dear Drs. TWiV,
I hope this correspondence finds you all well. I just finished listening to TWiV 363 (yes, it took me a few days as being a full-time father, student, and employee require a bit of time). Simply stated, I love TWiV!!! I first came across this podcast while searching for information about a report which I had to give on bacteriophage in my microbiology course at the local community college. Since that time, I have been an avid consumer of TWiV and recently decided to branch out into the other TWiX-casts. All of them are simply great!
You may remember me from TWiV 326 (my proud picture of “the happy guy in the middle”). The encouragement given by Drs. Racaniello and Condit was, and is, incredibly supportive and sustaining (“Someone has to pick plaques!”).
I recently attended a Grad School Forum at UC Santa Barbara and surprisingly found myself much more competitive than I had expected. I attribute this to two specific areas; my dear children (who have the “opportunity” to partake of TWiV during the morning/afternoon drives to/from school) who constantly push me to be better, and to the fabulous Drs. TWiX for stimulating excitement and wonder every week through a new podcast. My anticipation of the TWiV email notifying me of a new episode parallels that of a childhood Christmas morning. My aspirations of being a “future virologist” have become solidified!!!
Thank you all – Vincent, Alan, Kathy, Rich and Dickson – for your hard work, diligence and sharing of knowledge.
CSU-Bakersfield (Bakersfield, CA)
It is currently 61F (16.1C), sunny, wind 2mph, pollen 1.9, UV 4, air quality index 16.
Or for Alan; KBFL 182054Z 03003KT 10SM CLR 16/00 A3019 RMK AO2 SLP221 T01560000 58030
Dear Twiv team,
Hello! I am a 2nd year graduate student and new to the field of virology! So far, I’m hooked.
During a meeting today we were discussing how we could analyze viral RNA transcription in response to an inhibitory compound and I thought back to a TWIV episode from the summer where the paper discussed mentioned using northern blots as well as some way to pull out the RNA from the cells (perhaps with a biotin label or cap structure). For the life of me I cannot remember who authored the paper and I can’t seem to find it. Any help identifying this paper would be much appreciated!
Look forward to your next podcast!
Hi TWIV team,
In listening to older shows, I came across your discussion about the lady who wrote and said her pediatrician suggested she wait to give the hep b vaccine. You almost acted as though you did not believe her, though you did come around and say that she was going by advice.
Now I live in a relatively small town, and we only have 13 pediatricians here, and I know for certain that 11 of them recommend waiting until 6 months old to get the hep B vaccine. I have taken my own kids to 4 of them and other friends have taken theirs to some of the others, and we all have the same story. Of course we are all low risk and so is this area in general, so that may have a lot to do with it. Personally we did wait and there were no bad things happening because of it.
I abhor those who refuse to take vaccines and in this case none of us refused any of them, we just delayed one. In truth I do not think we were irresponsible, but had any of us not had the vaccine that would have been. I think you folks need to understand that people are only going by the best information they have, and pediatricians ARE giving this advice!!! You can not try to make folks feel like bad parents for following that advice!
It’s a chilly 60F (15.6C) here in Berkeley, CA.
Upon listening to TWiV 323’s discussion of a paper on changes in the fecal viromes of IBD sufferers, I too felt uneasy about the strong conclusions made based on the sequencing data, and was reminded of a common error of data analysis first discussed in the psychological sciences.
To paraphrase Rozeboom’s 1960 (Psychological Bulletin) and Meehl’s 1967 (Philosophy of Science), any sufficiently precise measurement of any feature of a biological system will reveal statistically significant differences between an experimental and a control group due to the inherent interconnectedness of complex biological systems. The rejection of a null hypothesis alone, therefore, should be regarded lightly, particularly in the case when highly detailed and precise data is gathered.
Since the human gut is exactly such a complex, interconnected system, any disease state will likely result in a statistically significant change in the richness of the virome (or the diversity of the microbiome, or indeed any other possible measurement) compared to healthy controls, particularly when the data in question are so detailed, as in this case. The sequencing experiments described in the IBD virome paper were bound to produce some statistically significant results since the gathering and comparison of so many data allows the formation of so many null hypotheses. The findings are therefore unsurprising, and perhaps not informative.
This is not to criticize too harshly this paper in particular, as we have been guilty as a field of regularly ignoring this error of data analysis, particularly with respect to deep sequencing data. Biological scientists must always remember, as Meehl explains, that “[i]t is important to keep clear the distinction between the substantive theory of interest and the statistical hypothesis which is derived from it.” A statistically significant difference does not a biological theory make; only the accumulation and careful assimilation of data from many related experiments, not a single statistical test, constitutes a scientific result.
Thank you all for sharing your thoughtful and thought-provoking discussions!
Hello, Team Twiv,
I love the podcasts and would like to make a request.
Can Twiv please include a brief episode on Oncolytic Viruses?
Please consider my request.
A couple of weeks ago, in the middle of the night, my restless mind was overtaken by an image of TWIV as a weekly Big Band radio show. Here’s a write-up of what my sleeping subconscious produced:
Introducing … The TWIV Band
Out front is Vinnie Racaniello on clarinet, the band’s founder and leader. A veteran performer in this and other bands, he fills each week’s show with just the right mix of familiar standards, old favorites and recent releases. TWIV is THE place to hear the latest hits. Vinnie occasionally invites members of other bands to sit in, giving them a chance to both perform solo and to jam with the TWIV band.
Vinnie always starts his shown with his signature tune, “How’s Your Weather?” This song, interestingly, is written in both the key of C and the key of F. After a short solo of the tune’s opening theme, Vinnie brings in each band member one at a time to play their own variation on the theme, until the whole room’s rocking.
Sitting at the foot of the bandstand is “Django” Despommier. As his nickname suggests, he’s almost a reincarnation of that pioneer Gypsy jazz guitarist. His steady background strumming occasionally breaks into unique and surprising improvisations that both echo his early roots and set a high standard for musical exploration. Also, like the original Django, he’ll often take off for parts unknown without much warning.
Alan Dove is on saxophone. He started out in Vinnie’s group early on, but moved into the recording side as a freelance session man. His versatility in that arena often brings musical elements from other genres to the weekly show. Alan’s signature saxophone style is renowned for his injecting occasional short musical notes that elicit laughter and/or groans.
Rich Condit, on bass, recently disbanded his own group after many years, and now we can only hear him on TWIV. His bass provides a solid underpinning for the band, while his solo work contains delightful and deep musical insights into a composition. Rich’s variations on the show’s opening theme are invariably bright and sunny.
Kathy Spindler, on keyboard, is the newest member of the band. Although sometimes drowned out when the rest of the group is jazzing it up, she more than holds her own when she breaks into a solo in the piano’s upper registers. Kathy has outstanding ensemble instincts, and is able to gently bring the group back together before they get lost in their improvisations.
Thanks to Vinnie’s own musical flair, his insightful leadership and his ability to recruit top talent, the TWIV show is not to be missed.
– Tom in Austin.
Thought this would be a good twiv listener pick of the week. Or a
Lifetime movie. Reads like it would work either way.
Weather in the St. Louis area is 49F, Wind SW 9mph, humidity 66%,
Dew Point 38F, pressure 29.74 inches, visibility 9.0 miles, UV index 0,
sunrise 6:49 am, sunset 4:49pm
Hi TWiV team,
Here is my listener’s pick of the week.
Hope you all enjoy!
University of Florida